Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01006803.1 Corchorus capsularis cultivar CVL-1 contig06824, 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, 619

Length: 1032
ACGTcount: A:0.25, C:0.18, G:0.18, T:0.40


Found at i:389 original size:154 final size:154

Alignment explanation


    Indices: 1--1032  Score: 1565
    Period size: 154  Copynumber: 6.7  Consensus size: 154

                                                         *                   
          1 AACCAAGAAAGCTTTTCTTCTAATTGTTTACGACCTAACTATAATCATTTTGATGAGATTAGTCC
          1 AACCAAGAAAGCTTTTCTTCTAATTGTTTACGACCTAACTATAATTATTTTGATGAGATTAGTCC

                              *                         *            *       
         66 ATTGTGAAGTTTTTAGCTAATTCAGAACACTTTTTATTTCGGGCTTTTCGGGGCCCATTAGTGCT
         66 ATTGTGAAGTTTTTAGCTCATTCAGAACACTTTTTATTTCGGGCCTTTCGGGGCCCAGTAGTGCT

                        *   *     **
        131 GTTTTGAATCGGCTTCGATTTGTA
        131 GTTTTGAATCGGTTTCAATTTGGC

                  *               *        * *                     *         
        155 AACC-ACAAAGCTTTTCTT-TCCATTGTTTATGGCCTAACTATAATTATTTTGATAAGATTAGTC
          1 AACCAAGAAAGCTTTTCTTCT-AATTGTTTACGACCTAACTATAATTATTTTGATGAGATTAGTC

                                                                             
        218 CATTGTGAAGTTTTTAGCTCATTCAGAACACTTTTTATTTCGGGCCTTTCGGGGCCCAGTAGTGC
         65 CATTGTGAAGTTTTTAGCTCATTCAGAACACTTTTTATTTCGGGCCTTTCGGGGCCCAGTAGTGC

                  *                  
        283 TGTTTTAAATCGGTTTCAATTTGGC
        130 TGTTTTGAATCGGTTTCAATTTGGC

                                                                             
        308 AACCAAGAAAGCTTTTCTTCTAATTGTTTACGACCTAACTATAATTATTTTGATGAGATTAGTCC
          1 AACCAAGAAAGCTTTTCTTCTAATTGTTTACGACCTAACTATAATTATTTTGATGAGATTAGTCC

                                                                 *           
        373 ATTGTGAAGTTTTTAGCTCATTCAGAACACTTTTTATTTCGGGCCTTTCGGGGACCAGTAGTGCT
         66 ATTGTGAAGTTTTTAGCTCATTCAGAACACTTTTTATTTCGGGCCTTTCGGGGCCCAGTAGTGCT

                                     
        438 GTTTTGAATCGGCTTT-AATTTGGC
        131 GTTTTGAATCGG-TTTCAATTTGGC

              **                                                             
        462 AAAGAAGAAAGCTTTTCTTCTAATTGTTTACGACCTAACTATAATTATTTTGATGAGATTAGTCC
          1 AACCAAGAAAGCTTTTCTTCTAATTGTTTACGACCTAACTATAATTATTTTGATGAGATTAGTCC

                                          *          *               *       
        527 ATTGTGAAGTTTTTAGCTCATTCAGAACACCTTTTATTTCGAGCCTTTCGGGGCCCATTAGTGCT
         66 ATTGTGAAGTTTTTAGCTCATTCAGAACACTTTTTATTTCGGGCCTTTCGGGGCCCAGTAGTGCT

                             *     * 
        592 GTTTTGAATC-GTCTTCGATTTGAC
        131 GTTTTGAATCGGT-TTCAATTTGGC

              * * *                        * *                               
        616 AAACGACAAAGCTTTTCTT-TCAATTGTTTATGGCCTAACTATAATTATTTTGATGAGATTAGTC
          1 AACCAAGAAAGCTTTTCTTCT-AATTGTTTACGACCTAACTATAATTATTTTGATGAGATTAGTC

                                              *                              
        680 CATTGTGAAGTTTTTAGCTCATTCAGAACACTTTATATTTCGGGCCTTTCGGGGCCCAGTAGTGC
         65 CATTGTGAAGTTTTTAGCTCATTCAGAACACTTTTTATTTCGGGCCTTTCGGGGCCCAGTAGTGC

                  *      *           
        745 TGTTTTAAATCGGCTTCAATTTGGC
        130 TGTTTTGAATCGGTTTCAATTTGGC

                                                         *      *     *      
        770 AACCAAGAAAGCTTTTCTTCTAATTGTTTACGACCTAACTATAATCATTTTGGTGAGAATAGTCC
          1 AACCAAGAAAGCTTTTCTTCTAATTGTTTACGACCTAACTATAATTATTTTGATGAGATTAGTCC

                                          *                          *       
        835 ATTGTGAAGTTTTTAGCTCATTCAGAACACCTTTTATTTCGGGCCTTTCGGGGCCCATTAGTGCT
         66 ATTGTGAAGTTTTTAGCTCATTCAGAACACTTTTTATTTCGGGCCTTTCGGGGCCCAGTAGTGCT

                             *       
        900 GTTTTGAATC-GTCTTCGATTTGGC
        131 GTTTTGAATCGGT-TTCAATTTGGC

              * * *               *        * *                               
        924 AAACGACAAAGCTTTTCTT-TCCATTGTTTATGGCCTAACTATAATTATTTTGATGAGATTAGTC
          1 AACCAAGAAAGCTTTTCTTCT-AATTGTTTACGACCTAACTATAATTATTTTGATGAGATTAGTC

                                                  *      
        988 CATTGTGAAGTTTTTAGCTCATTCAGAACTACTTTTTAGTTCGGG
         65 CATTGTGAAGTTTTTAGCTCATTCAGAAC-ACTTTTTATTTCGGG


Statistics
Matches: 799,  Mismatches: 67, Indels: 23
        0.90            0.08        0.03

Matches are distributed among these distances:
 152    2  0.00
 153  143  0.18
 154  635  0.79
 155   19  0.02

ACGTcount: A:0.25, C:0.18, G:0.18, T:0.40


Consensus pattern (154 bp):   
AACCAAGAAAGCTTTTCTTCTAATTGTTTACGACCTAACTATAATTATTTTGATGAGATTAGTCC
ATTGTGAAGTTTTTAGCTCATTCAGAACACTTTTTATTTCGGGCCTTTCGGGGCCCAGTAGTGCT
GTTTTGAATCGGTTTCAATTTGGC

Found at i:872 original size:462 final size:462

Alignment explanation


    Indices: 5--1030  Score: 1770
    Period size: 462  Copynumber: 2.2  Consensus size: 462

          1 AACC

                                                     *                       
          5 AAGAAAGCTTTTCTTCTAATTGTTTACGACCTAACTATAATCATTTTGATGAGATTAGTCCATTG
          1 AAGAAAGCTTTTCTTCTAATTGTTTACGACCTAACTATAATTATTTTGATGAGATTAGTCCATTG

                          *                      *  *                        
         70 TGAAGTTTTTAGCTAATTCAGAACACTTTTTATTTCGGGCTTTTCGGGGCCCATTAGTGCTGTTT
         66 TGAAGTTTTTAGCTCATTCAGAACACTTTTTATTTCGAGCCTTTCGGGGCCCATTAGTGCTGTTT

                              *                     *                        
        135 TGAATCGGCTTCGATTTGTAAACCACAAAGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATT
        131 TGAATCGGCTTCGATTTGCAAACCACAAAGCTTTTCTTTCAATTGTTTATGGCCTAACTATAATT

                                                                *            
        200 ATTTTGATAAGATTAGTCCATTGTGAAGTTTTTAGCTCATTCAGAACACTTTTTATTTCGGGCCT
        196 ATTTTGATAAGATTAGTCCATTGTGAAGTTTTTAGCTCATTCAGAACACTTTATATTTCGGGCCT

                                           *                                 
        265 TTCGGGGCCCAGTAGTGCTGTTTTAAATCGGTTTCAATTTGGCAACCAAGAAAGCTTTTCTTCTA
        261 TTCGGGGCCCAGTAGTGCTGTTTTAAATCGGCTTCAATTTGGCAACCAAGAAAGCTTTTCTTCTA

                                   *            *                            
        330 ATTGTTTACGACCTAACTATAATTATTTTGATGAGATTAGTCCATTGTGAAGTTTTTAGCTCATT
        326 ATTGTTTACGACCTAACTATAATCATTTTGATGAGAATAGTCCATTGTGAAGTTTTTAGCTCATT

                    *                                                 *      
        395 CAGAACACTTTTTATTTCGGGCCTTTCGGGGACCAGTAGTGCTGTTTTGAATCGGCTTTAATTTG
        391 CAGAACACCTTTTATTTCGGGCCTTTCGGGGACCAGTAGTGCTGTTTTGAATCGGCTTCAATTTG

                   
        460 GCAAA-G
        456 GCAAACG

                                                                             
        466 AAGAAAGCTTTTCTTCTAATTGTTTACGACCTAACTATAATTATTTTGATGAGATTAGTCCATTG
          1 AAGAAAGCTTTTCTTCTAATTGTTTACGACCTAACTATAATTATTTTGATGAGATTAGTCCATTG

                                      *                                      
        531 TGAAGTTTTTAGCTCATTCAGAACACCTTTTATTTCGAGCCTTTCGGGGCCCATTAGTGCTGTTT
         66 TGAAGTTTTTAGCTCATTCAGAACACTTTTTATTTCGAGCCTTTCGGGGCCCATTAGTGCTGTTT

                   *                *                                        
        596 TGAATCGTCTTCGATTTGACAAACGACAAAGCTTTTCTTTCAATTGTTTATGGCCTAACTATAAT
        131 TGAATCGGCTTCGATTTG-CAAACCACAAAGCTTTTCTTTCAATTGTTTATGGCCTAACTATAAT

                     *                                                       
        661 TATTTTGATGAGATTAGTCCATTGTGAAGTTTTTAGCTCATTCAGAACACTTTATATTTCGGGCC
        195 TATTTTGATAAGATTAGTCCATTGTGAAGTTTTTAGCTCATTCAGAACACTTTATATTTCGGGCC

                                                                             
        726 TTTCGGGGCCCAGTAGTGCTGTTTTAAATCGGCTTCAATTTGGCAACCAAGAAAGCTTTTCTTCT
        260 TTTCGGGGCCCAGTAGTGCTGTTTTAAATCGGCTTCAATTTGGCAACCAAGAAAGCTTTTCTTCT

                                           *                                 
        791 AATTGTTTACGACCTAACTATAATCATTTTGGTGAGAATAGTCCATTGTGAAGTTTTTAGCTCAT
        325 AATTGTTTACGACCTAACTATAATCATTTTGATGAGAATAGTCCATTGTGAAGTTTTTAGCTCAT

                                            *   *                  *    *    
        856 TCAGAACACCTTTTATTTCGGGCCTTTCGGGGCCCATTAGTGCTGTTTTGAATCGTCTTCGATTT
        390 TCAGAACACCTTTTATTTCGGGCCTTTCGGGGACCAGTAGTGCTGTTTTGAATCGGCTTCAATTT

                    
        921 GGCAAACG
        455 GGCAAACG

              *               *        * *                                   
        929 -ACAAAGCTTTTCTT-TCCATTGTTTATGGCCTAACTATAATTATTTTGATGAGATTAGTCCATT
          1 AAGAAAGCTTTTCTTCT-AATTGTTTACGACCTAACTATAATTATTTTGATGAGATTAGTCCATT

                                              *    
        992 GTGAAGTTTTTAGCTCATTCAGAACTACTTTTTAGTTCG
         65 GTGAAGTTTTTAGCTCATTCAGAAC-ACTTTTTATTTCG

       1031 GG


Statistics
Matches: 534,  Mismatches: 27, Indels: 6
        0.94            0.05        0.01

Matches are distributed among these distances:
 461  143  0.27
 462  379  0.71
 463   12  0.02

ACGTcount: A:0.25, C:0.17, G:0.18, T:0.40


Consensus pattern (462 bp):   
AAGAAAGCTTTTCTTCTAATTGTTTACGACCTAACTATAATTATTTTGATGAGATTAGTCCATTG
TGAAGTTTTTAGCTCATTCAGAACACTTTTTATTTCGAGCCTTTCGGGGCCCATTAGTGCTGTTT
TGAATCGGCTTCGATTTGCAAACCACAAAGCTTTTCTTTCAATTGTTTATGGCCTAACTATAATT
ATTTTGATAAGATTAGTCCATTGTGAAGTTTTTAGCTCATTCAGAACACTTTATATTTCGGGCCT
TTCGGGGCCCAGTAGTGCTGTTTTAAATCGGCTTCAATTTGGCAACCAAGAAAGCTTTTCTTCTA
ATTGTTTACGACCTAACTATAATCATTTTGATGAGAATAGTCCATTGTGAAGTTTTTAGCTCATT
CAGAACACCTTTTATTTCGGGCCTTTCGGGGACCAGTAGTGCTGTTTTGAATCGGCTTCAATTTG
GCAAACG
Done.