Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01006252.1 Corchorus capsularis cultivar CVL-1 contig06271, 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, 625

Length: 1043
ACGTcount: A:0.22, C:0.19, G:0.21, T:0.39


Found at i:952 original size:153 final size:153

Alignment explanation


    Indices: 1--1043  Score: 1560
    Period size: 155  Copynumber: 6.7  Consensus size: 153

                                                                             
          1 CCTAACTATAATCGATTTTGGTGTAGATTAGTCCATCGTGTAAGTTTTTAGCTCATTCAGTAACA
          1 CCTAACTATAATC-ATTTTGGTG-AGATTAGTCCAT-GTG-AAGTTTTTAGCTCATTCAG-AACA

                  *                                  *                  *   *
         66 CTTGTTTTTTCGGGCCTTTCGGGGCCCATTAGTGCTGTTTTTAATCGGCTTCGAGTTTGGGAAAG
         61 CTTGTTATTTCGGGCCTTTCGGGGCCCATTAGTGCTGTTTTGAATCGGCTTCGA-TTTGGCAAAC

                                 *       
        131 CACAAAGCTTTTCTTTCAATTTTTTACGG
        125 CACAAAGCTTTTCTTTCAATTGTTTACGG

                                                                             
        160 CCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTC-GAAACACTT
          1 CCTAACTATAATCATTTTGGTGAGATTAGTCCA-TGTGAAGTTTTTAGCTCATTCAG-AACACTT

                                                                     *      *
        224 GTTATTTCTGGGCCTTTCGGGGCCCATTAGTGCTGTTTTGAATCGGCTTCGATTTGGGAAACCAT
         64 GTTATTTC-GGGCCTTTCGGGGCCCATTAGTGCTGTTTTGAATCGGCTTCGATTTGGCAAACCAC

                                      
        289 AAAGCTTTTCTTTCAATTGTTTACGG
        128 AAAGCTTTTCTTTCAATTGTTTACGG

                                                          *                  
        315 CCTAACTATAATCATTTTGGTGAGATTAGTCCAATGTGAAGTTTTTCGCTCATTCAGAACACTTG
          1 CCTAACTATAATCATTTTGGTGAGATTAGTCC-ATGTGAAGTTTTTAGCTCATTCAGAACACTTG

                      *            *                                     *   
        380 TTATTTCGGGTCTTTCGGGGCCCGTTAGTGCTGTTTTGAATTCGGCTTCGATTTGGCAAACGACA
         65 TTATTTCGGGCCTTTCGGGGCCCATTAGTGCTGTTTTGAA-TCGGCTTCGATTTGGCAAACCACA

                        *   *       *
        445 AAGCTTTTCTTTTAATGGTTTACGA
        129 AAGCTTTTCTTTCAATTGTTTACGG

                                 *           *                               
        470 CCTAACTATAATCATTTTGGTTAGATTAGTCCGTTGTGAAGTTTTTAGCTCATTCAGAACACTTG
          1 CCTAACTATAATCATTTTGGTGAGATTAGTCC-ATGTGAAGTTTTTAGCTCATTCAGAACACTTG

                  *                               *                          
        535 TTATTTTGGGCCTTTCGGGGCCCATTAGTGCTGTTTTGCATCGGCTTCGATTTGGCAAACCACAA
         65 TTATTTCGGGCCTTTCGGGGCCCATTAGTGCTGTTTTGAATCGGCTTCGATTTGGCAAACCACAA

                    *              *
        600 AGCTTTTCCTTCAATTGTTTACGA
        130 AGCTTTTCTTTCAATTGTTTACGG

                                               *                             
        624 CCTAACTATAATCATTTTGGTGAGATTAGTCCATCATGAAG-TTTTAGCTCATTCAGAACAC-TG
          1 CCTAACTATAATCATTTTGGTGAGATTAGTCCAT-GTGAAGTTTTTAGCTCATTCAGAACACTTG

              *                             *                 *    *   *     
        687 TTTTTTCGGGCCTTTCGGGGCCCATTAGTGCTATTTTGAATCGGCTTCGAGTTGGGAAAGCACTA
         65 TTATTTCGGGCCTTTCGGGGCCCATTAGTGCTGTTTTGAATCGGCTTCGATTTGGCAAACCAC-A

                                     
        752 AAGC-TTTCTTTCAATT-TTTACGG
        129 AAGCTTTTCTTTCAATTGTTTACGG

                                               *                   *         
        775 CCTAACTATAATCATTTTGGTGAGATTAGTCCACTTTGAAGTTTTTAGCTCATTCGGAACACTTG
          1 CCTAACTATAATCATTTTGGTGAGATTAGTCCA-TGTGAAGTTTTTAGCTCATTCAGAACACTTG

                     *                 *                                     
        840 TTATTTCGGTCCTTTCGGGGCCCATTAATGCTG-TTTGAATCGGCTTCGATTTGGCAAACCACAA
         65 TTATTTCGGGCCTTTCGGGGCCCATTAGTGCTGTTTTGAATCGGCTTCGATTTGGCAAACCACAA

                 *               *  
        904 AGCTTGTCTTTCAATTGTTTATGG
        130 AGCTTTTCTTTCAATTGTTTACGG

                       *                                                     
        928 CCTAACTATAAACATTTTGGTGAGATTAGTCCATTGTGAACG-TTTTAGCTCATTCAGAACACTT
          1 CCTAACTATAATCATTTTGGTGAGATTAGTCCA-TGTGAA-GTTTTTAGCTCATTCAGAACACTT

               *                                         *      
        992 GTTGTTTCGGGCCTTTCGGGGCCCATTAGTGCTGTTTTGGAATCGTCTTCGA
         64 GTTATTTCGGGCCTTTCGGGGCCCATTAGTGCTGTTTT-GAATCGGCTTCGA


Statistics
Matches: 811,  Mismatches: 58, Indels: 34
        0.90            0.06        0.04

Matches are distributed among these distances:
 151   49  0.06
 152  126  0.16
 153  152  0.19
 154  116  0.14
 155  270  0.33
 156   61  0.08
 157   14  0.02
 158   10  0.01
 159   13  0.02

ACGTcount: A:0.22, C:0.19, G:0.21, T:0.39


Consensus pattern (153 bp):   
CCTAACTATAATCATTTTGGTGAGATTAGTCCATGTGAAGTTTTTAGCTCATTCAGAACACTTGT
TATTTCGGGCCTTTCGGGGCCCATTAGTGCTGTTTTGAATCGGCTTCGATTTGGCAAACCACAAA
GCTTTTCTTTCAATTGTTTACGG
Done.