Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01004465.1 Corchorus capsularis cultivar CVL-1 contig04473, 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, 610

Length: 1017
ACGTcount: A:0.23, C:0.18, G:0.18, T:0.41


Found at i:406 original size:155 final size:155

Alignment explanation


    Indices: 1--1006  Score: 1355
    Period size: 155  Copynumber: 6.4  Consensus size: 155

                  *  *     *                      *                          
          1 TCTTTCAATAGTTTACGGCCTAACTATAATTATTTTTGGTGAGATTAGTCCACTGTGAAGTTTTT
          1 TCTTTCCATTGTTTATGGCCTAACTATAATTA-TTTTGATGAGATTAGTCCACTGTGAAGTTTTT

                                                              *              
         66 AGC-TCATTCAGAACACTTGTTATTTCAGGCCTTTCGGGGCCCATTAGTGTTATTTTGAATCGTA
         65 AGCTTCATTCAGAACACTTGTTATTTCAGGCCTTTCGGGGCCCATTAGTGCTATTTTGAATCGTA

                                *     
        130 TTCGATTTGGCAAACCACAATGCTTT
        130 TTCGATTTGGCAAACCACAAAGCTTT

                                    *              *           *         *   
        156 TCTTTCCA-TGTTTATGGCCTAACAATAATTATTTTGATAAGATTAGTCCATTGTGAAGTCGTTT
          1 TCTTTCCATTGTTTATGGCCTAACTATAATTATTTTGATGAGATTAGTCCACTGTGAAGT-TTTT

                     *                 *                          *          
        220 AGC-TCATTTAGAACACTTGTTATTTCGGGCCTTTCGGGGCCCATTAGTGCTATCTTGAATCGTA
         65 AGCTTCATTCAGAACACTTGTTATTTCAGGCCTTTCGGGGCCCATTAGTGCTATTTTGAATCGTA

                                       
        284 TTCGATTTGGCAAACCACAATA-CTTT
        130 TTCGATTTGGCAAACCACAA-AGCTTT

                                                 *             *             
        310 TCTTTCCATTGTTTATGGCCTAACTATAATTATTTTGTTGAGATTAGTCCATTGTGAAGTTTTTA
          1 TCTTTCCATTGTTTATGGCCTAACTATAATTATTTTGATGAGATTAGTCCACTGTGAAGTTTTTA

                     *                         *    *          *     *     * 
        375 GCTTCATTCGGAACACTTGTTATTTCAGGCCTTTCAGGGCGCATTAGTGCTGTTTTGTATCGTCT
         66 GCTTCATTCAGAACACTTGTTATTTCAGGCCTTTCGGGGCCCATTAGTGCTATTTTGAATCGTAT

                 *  *    * *         
        440 TCGATATGACAAATCGCAAAGCTTT
        131 TCGATTTGGCAAACCACAAAGCTTT

                               *          *      *            *              
        465 TCTTTCCATTGTTTATGGCATAACTATAATCATTTTGGTGAGATTAGTCCGCTGTGAAGTTTTTT
          1 TCTTTCCATTGTTTATGGCCTAACTATAATTATTTTGATGAGATTAGTCCACTGTGAAG-TTTTT

                                                    * *          *     *     
        530 AGCTTCATTCAGAACACTTGTTATTTCAGGCCTTTCAGGGTCGCATTAGTGCTGTTTTGTATCGT
         65 AGCTTCATTCAGAACACTTGTTATTTCAGGCCTTTC-GGGGCCCATTAGTGCTATTTTGAATCGT

            *          *      *       * 
        595 CTTCGATTATGACAAACCGCAAAGCTAT
        129 ATTCGATT-TGGCAAACCACAAAGCTTT

                                *                 *                          
        623 TCTTTCCATTGTTTATGGGCTTAACTATAATTATTTTGGTGAGATTAGTCCACTGTGAAGTTTTT
          1 TCTTTCCATTGTTTAT-GGCCTAACTATAATTATTTTGATGAGATTAGTCCACTGTGAAGTTTTT

                                       *         *          *   *           *
        688 AGC-TCATTCAGAACACTTGTTATTTCGGGCCTTTCGAGGCCCATTAGAGCTGTTTTGAATCGGC
         65 AGCTTCATTCAGAACACTTGTTATTTCAGGCCTTTCGGGGCCCATTAGTGCTATTTTGAATC-GT

                                         
        752 A-TCGTATTTAGGCAAACCACAAAGCTTT
        129 ATTCG-ATTT-GGCAAACCACAAAGCTTT

                               *                                  *          
        780 TCTTTCCAATTGTTTATAGTCCTAACTATAATTATTTTGATGAGAGTTAGTCCATTGTGAAGTTT
          1 TCTTTCC-ATTGTTTAT-GGCCTAACTATAATTATTTTGATGAGA-TTAGTCCACTGTGAAG-TT

                                           *          *                      
        845 TTTAGCTTCATTCAGAACTACTTGTTATTTCGGGCCTTTCGGTGCCCATTAGTGCTAGTTTTGAA
         62 TTTAGCTTCATTCAGAAC-ACTTGTTATTTCAGGCCTTTCGGGGCCCATTAGTGCTA-TTTTGAA

                                      *     
        910 TCGTATAT-GATTTGGCAAACCACAATGCTTT
        125 TCGTAT-TCGATTTGGCAAACCACAAAGCTTT

                                                                             
        941 TCTTTCCATTGTTTATGGCCTAACTATAATTATTTTGATGAGATTAGTCCA-TGTG-AGTTTTTA
          1 TCTTTCCATTGTTTATGGCCTAACTATAATTATTTTGATGAGATTAGTCCACTGTGAAGTTTTTA

               
       1004 GCT
         66 GCT

       1007 CTTTCAGTAA


Statistics
Matches: 764,  Mismatches: 67, Indels: 40
        0.88            0.08        0.05

Matches are distributed among these distances:
 153   25  0.03
 154  122  0.16
 155  190  0.25
 156   67  0.09
 157   94  0.12
 158   82  0.11
 159   81  0.11
 160   17  0.02
 161   35  0.05
 162   40  0.05
 163   10  0.01
 164    1  0.00

ACGTcount: A:0.23, C:0.18, G:0.18, T:0.41


Consensus pattern (155 bp):   
TCTTTCCATTGTTTATGGCCTAACTATAATTATTTTGATGAGATTAGTCCACTGTGAAGTTTTTA
GCTTCATTCAGAACACTTGTTATTTCAGGCCTTTCGGGGCCCATTAGTGCTATTTTGAATCGTAT
TCGATTTGGCAAACCACAAAGCTTT

Done.