Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01009643.1 Corchorus olitorius cultivar O-4 contig09675, 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: 4226
ACGTcount: A:0.33, C:0.15, G:0.16, T:0.36


Found at i:832 original size:356 final size:357

Alignment explanation


    Indices: 156--1109  Score: 1443
    Period size: 360  Copynumber: 2.7  Consensus size: 357

        146 GATTTTTTGC

                      *    *        *                    *                   
        156 CTAAAAACGCTTTCCAGAGTCCCGGCTCAATTTTGCATGATTTTTGGCGTAAAGACTCCTTGAAA
          1 CTAAAAACGCGTTCCGGAGTCCCGACTCAATTTTGCATGATTTTTAGCGTAAAGACTCCTTGAAA

                                       *                            *        
        221 TATCTATATTCATCGTACCAAATCTCAACCACGTTGTATATAAGGATTTGTTTTTATGAGCATCT
         66 TATCTATATTCATCGTACCAAATCTCAGCCACGTTGTATATAAGGATTTGTTTTTACGAGCATCT

                                                                             
        286 GAATCTTTATTTTGATTTAATTAGAAATAAATACGGAAAAAAATGGAAAAACGATATTAGAAGCG
        131 GAATCTTTATTTTGATTTAATTAGAAATAAATACGGAAAAAAATGGAAAAACGATATTAGAAGCG

              *                                          *                   
        351 TAAAAAAACCCTTCAACTTTTTTTGGCGTTGAATTATATATTTTTCTGAGTATTGTGGCAAAAAA
        196 T-GAAAAACCCTTCAACTTTTTTTGGCGTTGAATTATATATTTTTATGAGTATTGTGGCAAAAAA

                                  *                    *    *                
        416 TTAAGGAAAAACCTTTCGGGTCTATTTTTGCAAAATTTTAGCCGAAATTGTGTA-TTTTTTTT-C
        260 TTAAGGAAAAACCTTTCGGGTCAATTTTTGCAAAATTTTAGCCAAAATCGTGTATTTTTTTTTCC

                    *               *       * 
        479 AACGAAATTGTGTACGT-TATCATTGTTTTTGGG
        325 AACGAAATCGTGTAC-TATATCATGGTTTTTGAG

                   *        *     *      *    *          *                   
        512 CTAAAAAGGCGTTCCGTAGTCCTGACTCATTTTTCCATGATTTTTTGCGTAAAGACTCCTTGAAA
          1 CTAAAAACGCGTTCCGGAGTCCCGACTCAATTTTGCATGATTTTTAGCGTAAAGACTCCTTGAAA

                   *                                                         
        577 TATCTATTTTCATCGTACCAAATCTCAGCCACGTTGTATATAAGGATTTGTTTTTACGAGCATCT
         66 TATCTATATTCATCGTACCAAATCTCAGCCACGTTGTATATAAGGATTTGTTTTTACGAGCATCT

                                                                             
        642 GAATCTTTATTTTGATTTAATTAGAAATAAATACGGAAAAAAA-GGAAAAACGATATTAGAAGCG
        131 GAATCTTTATTTTGATTTAATTAGAAATAAATACGGAAAAAAATGGAAAAACGATATTAGAAGCG

                                                                             
        706 TGAAAAACCCTTCAACTTTTTTTGGCGTTGAATTATATATTTTTATGAGTATTGTGGCAAAAAAA
        196 TGAAAAACCCTTCAACTTTTTTTGGCGTTGAATTATATATTTTTATGAGTATTGTGGC-AAAAAA

              *             *                                                
        771 TTGAGGAAAAACCTTTTGGGTCAATTTTTGCAAAATTTTAGCCAAAATCGTGTACTTTTTTTTTC
        260 TTAAGGAAAAACCTTTCGGGTCAATTTTTGCAAAATTTTAGCCAAAATCGTGTA-TTTTTTTTTC

                                             *  
        836 CAACGAAATCGTGTACTAACTATCATGGTTTTTTAG
        324 CAACGAAATCGTGTACT-A-TATCATGGTTTTTGAG

                                    *  *                    *        *       
        872 CTAAAAACGCGTTCCGGAGTCCCGGCTAAATTTTGCATGATTTTTAGCTTAAAGACTTCTTGAAA
          1 CTAAAAACGCGTTCCGGAGTCCCGACTCAATTTTGCATGATTTTTAGCGTAAAGACTCCTTGAAA

                       *                                                   * 
        937 TATCTATATTCTTCGTACCAAATCTCAGCCACGTTGTATATAAGGATTTGTTTTTACGAGCATAT
         66 TATCTATATTCATCGTACCAAATCTCAGCCACGTTGTATATAAGGATTTGTTTTTACGAGCATCT

                 *      *            *  *   *                    *           
       1002 GAAT-ATTATTTCGATTTAATTAGATATTAATTCGGAAAAAAAATGGAAAAACAATATTAGAAGC
        131 GAATCTTTATTTTGATTTAATTAGAAATAAATACGG-AAAAAAATGGAAAAACGATATTAGAAGC

            *    * *   *                                 
       1066 ATGAATAGCCCATCAA-TTTTTTTGGCGTTGAATTATATATTTTT
        195 GTGAAAAACCCTTCAACTTTTTTTGGCGTTGAATTATATATTTTT

       1110 TCTAAATATT


Statistics
Matches: 543,  Mismatches: 46, Indels: 14
        0.90            0.08        0.02

Matches are distributed among these distances:
 354   55  0.10
 355   77  0.14
 356  161  0.30
 357    9  0.02
 358   15  0.03
 359   26  0.05
 360  169  0.31
 361   31  0.06

ACGTcount: A:0.33, C:0.14, G:0.16, T:0.37


Consensus pattern (357 bp):   
CTAAAAACGCGTTCCGGAGTCCCGACTCAATTTTGCATGATTTTTAGCGTAAAGACTCCTTGAAA
TATCTATATTCATCGTACCAAATCTCAGCCACGTTGTATATAAGGATTTGTTTTTACGAGCATCT
GAATCTTTATTTTGATTTAATTAGAAATAAATACGGAAAAAAATGGAAAAACGATATTAGAAGCG
TGAAAAACCCTTCAACTTTTTTTGGCGTTGAATTATATATTTTTATGAGTATTGTGGCAAAAAAT
TAAGGAAAAACCTTTCGGGTCAATTTTTGCAAAATTTTAGCCAAAATCGTGTATTTTTTTTTCCA
ACGAAATCGTGTACTATATCATGGTTTTTGAG

Found at i:987 original size:360 final size:356

Alignment explanation


    Indices: 133--1109  Score: 1453
    Period size: 356  Copynumber: 2.7  Consensus size: 356

        123 CAAAAATGTT

                   *    * *                  *    *                          
        133 TACTAACCATCACGATTTTTTGCCTAAAAACGCTTTCCAGAGTCCCGGCTCAATTTTGCATGATT
          1 TACTAACTATCATGGTTTTTTG-CTAAAAACGCGTTCCGGAGTCCCGGCTCAATTTTGCATGATT

               *                                              *              
        198 TTTGGCGTAAAGACTCCTTGAAATATCTATATTCATCGTACCAAATCTCAACCACGTTGTATATA
         65 TTTAGCGTAAAGACTCCTTGAAATATCTATATTCATCGTACCAAATCTCAGCCACGTTGTATATA

                          *                                                  
        263 AGGATTTGTTTTTATGAGCATCTGAATCTTTATTTTGATTTAATTAGAAATAAATACGGAAAAAA
        130 AGGATTTGTTTTTACGAGCATCTGAATCTTTATTTTGATTTAATTAGAAATAAATACGGAAAAAA

                                     *                                       
        328 ATGGAAAAACGATATTAGAAGCGTAAAAAAACCCTTCAACTTTTTTTGGCGTTGAATTATATATT
        195 ATGGAAAAACGATATTAGAAGCGT-GAAAAACCCTTCAACTTTTTTTGGCGTTGAATTATATATT

               *                                         *                   
        393 TTTCTGAGTATTGTGGCAAAAAATTAAGGAAAAACCTTTCGGGTCTATTTTTGCAAAATTTTAGC
        259 TTTATGAGTATTGTGGCAAAAAATTAAGGAAAAACCTTTCGGGTCAATTTTTGCAAAATTTTAGC

             *    *                      *   
        458 CGAAATTGTGTATTTTTTTTCAACGAAATTGTG
        324 CAAAATCGTGTATTTTTTTTCAACGAAATCGTG

                          *       *        *        *     * *    *    *      
        491 TACGT---TATCATTGTTTTTGGGCTAAAAAGGCGTTCCGTAGTCCTGACTCATTTTTCCATGAT
          1 TAC-TAACTATCATGGTTTTT-TGCTAAAAACGCGTTCCGGAGTCCCGGCTCAATTTTGCATGAT

                *                          *                                 
        553 TTTTTGCGTAAAGACTCCTTGAAATATCTATTTTCATCGTACCAAATCTCAGCCACGTTGTATAT
         64 TTTTAGCGTAAAGACTCCTTGAAATATCTATATTCATCGTACCAAATCTCAGCCACGTTGTATAT

                                                                             
        618 AAGGATTTGTTTTTACGAGCATCTGAATCTTTATTTTGATTTAATTAGAAATAAATACGGAAAAA
        129 AAGGATTTGTTTTTACGAGCATCTGAATCTTTATTTTGATTTAATTAGAAATAAATACGGAAAAA

                                                                             
        683 AA-GGAAAAACGATATTAGAAGCGTGAAAAACCCTTCAACTTTTTTTGGCGTTGAATTATATATT
        194 AATGGAAAAACGATATTAGAAGCGTGAAAAACCCTTCAACTTTTTTTGGCGTTGAATTATATATT

                                      *             *                        
        747 TTTATGAGTATTGTGGCAAAAAAATTGAGGAAAAACCTTTTGGGTCAATTTTTGCAAAATTTTAG
        259 TTTATGAGTATTGTGGC-AAAAAATTAAGGAAAAACCTTTCGGGTCAATTTTTGCAAAATTTTAG

                                                 
        812 CCAAAATCGTGTACTTTTTTTTTCCAACGAAATCGTG
        323 CCAAAATCGTGTA--TTTTTTTT-CAACGAAATCGTG

                                                              *              
        849 TACTAACTATCATGGTTTTTTAGCTAAAAACGCGTTCCGGAGTCCCGGCTAAATTTTGCATGATT
          1 TACTAACTATCATGGTTTTTT-GCTAAAAACGCGTTCCGGAGTCCCGGCTCAATTTTGCATGATT

                  *        *                  *                              
        914 TTTAGCTTAAAGACTTCTTGAAATATCTATATTCTTCGTACCAAATCTCAGCCACGTTGTATATA
         65 TTTAGCGTAAAGACTCCTTGAAATATCTATATTCATCGTACCAAATCTCAGCCACGTTGTATATA

                                 *      *      *            *  *   *         
        979 AGGATTTGTTTTTACGAGCATATGAAT-ATTATTTCGATTTAATTAGATATTAATTCGGAAAAAA
        130 AGGATTTGTTTTTACGAGCATCTGAATCTTTATTTTGATTTAATTAGAAATAAATACGG-AAAAA

                       *           *    * *   *                              
       1043 AATGGAAAAACAATATTAGAAGCATGAATAGCCCATCAA-TTTTTTTGGCGTTGAATTATATATT
        194 AATGGAAAAACGATATTAGAAGCGTGAAAAACCCTTCAACTTTTTTTGGCGTTGAATTATATATT

               
       1107 TTT
        259 TTT

       1110 TCTAAATATT


Statistics
Matches: 557,  Mismatches: 50, Indels: 22
        0.89            0.08        0.03

Matches are distributed among these distances:
 354   55  0.10
 355   77  0.14
 356  170  0.31
 357   10  0.02
 358   18  0.03
 359   27  0.05
 360  169  0.30
 361   31  0.06

ACGTcount: A:0.32, C:0.15, G:0.16, T:0.37


Consensus pattern (356 bp):   
TACTAACTATCATGGTTTTTTGCTAAAAACGCGTTCCGGAGTCCCGGCTCAATTTTGCATGATTT
TTAGCGTAAAGACTCCTTGAAATATCTATATTCATCGTACCAAATCTCAGCCACGTTGTATATAA
GGATTTGTTTTTACGAGCATCTGAATCTTTATTTTGATTTAATTAGAAATAAATACGGAAAAAAA
TGGAAAAACGATATTAGAAGCGTGAAAAACCCTTCAACTTTTTTTGGCGTTGAATTATATATTTT
TATGAGTATTGTGGCAAAAAATTAAGGAAAAACCTTTCGGGTCAATTTTTGCAAAATTTTAGCCA
AAATCGTGTATTTTTTTTCAACGAAATCGTG
Done.