Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01011684.1 Corchorus olitorius cultivar O-4 contig11717, 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: 4412
ACGTcount: A:0.25, C:0.20, G:0.18, T:0.37


Found at i:2886 original size:154 final size:154

Alignment explanation


    Indices: 2473--4412  Score: 3142
    Period size: 154  Copynumber: 12.6  Consensus size: 154

       2463 GCTGATTGGA

                                       *       *         *                   
       2473 GAAGTTTTTAGCTCATTTGGAACACTTATTATTTTAGGCCTATCGGGGCCCATTAGTTCCGTTTT
          1 GAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGGGCCTATCGAGGCCCATTAGTTCCGTTTT

                                                    *        *               
       2538 GAATCGTCTTCGATTTGGCAACCCTCAATGCTTTTCTTTCTATTGTTTAAGGCCTAACTATAATC
         66 GAATCGTCTTCGATTTGGCAACCCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATC

                             *      
       2603 ATTTTGGTGAGATTAGTCCACTGT
        131 ATTTTGGTGAGATTAGTACACTGT

                                                            *    *      **   
       2627 GTAA-TTTTTAGCTCTATTTGGAACACTTGTTATTTTGGGCCTAAT-GGGGCCGATTAGTGACGT
          1 G-AAGTTTTTAGCTC-ATTTGGAACACTTGTTATTTTGGGCCT-ATCGAGGCCCATTAGTTCCGT

                                         *  *    *                      *   *
       2690 TTTGAATCGTCTTCGATTTGGCAACCCTCTATTCTTTGCTTTCCATTGTTTATGGCCTAATTATT
         63 TTTGAATCGTCTTCGATTTGGCAACCCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATA

                         *      *      
       2755 ATCATTTTGGTGATATTAGTCCACTGT
        128 ATCATTTTGGTGAGATTAGTACACTGT

                                                                             
       2782 GAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGGGCCTATCGAGGCCCATTAGTTCCGTTTT
          1 GAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGGGCCTATCGAGGCCCATTAGTTCCGTTTT

                                                                             
       2847 GAATCGTCTTCGATTTGGCAACCCTCAATG-TCTTTCTTTCCATTGTTTATGGCCTAACTATAAT
         66 GAATCGTCTTCGATTTGGCAACCCTCAATGCT-TTTCTTTCCATTGTTTATGGCCTAACTATAAT

                                   * 
       2911 CATTTTGGTGAGATTAGTACACTAT
        130 CATTTTGGTGAGATTAGTACACTGT

             *                                             *    *      **    
       2936 GTAGTTTTTAGCTCATTTGGAACTACTTGTTATTTTGGGCCTAAT-GGGGCCGATTAGTGACG-T
          1 GAAGTTTTTAGCTCATTTGGAAC-ACTTGTTATTTTGGGCCT-ATCGAGGCCCATTAGTTCCGTT

                                                                             
       2999 TTGAATCGTCTTCGATTTGGCAACCCTCAATGC-TTTC-TTCCATTGTTTATGGCCTAACTATAA
         64 TTGAATCGTCTTCGATTTGGCAACCCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAA

                                     * 
       3062 TCATTTTGGTGAGATTAGTACACTTAT
        129 TCATTTTGGTGAGATTAGTACAC-TGT

             *                     *                                         
       3089 GTAGTTTTTAAGCTCATTTGGAATACTTGTTATTTTGGGCCTATCGAGGCCCATTAGTTCCGTTT
          1 GAAGTTTTT-AGCTCATTTGGAACACTTGTTATTTTGGGCCTATCGAGGCCCATTAGTTCCGTTT

                                          *                           *   *  
       3154 TGAATCGTCTTCGATTTGGCAACCCTCAATTCTTTTCTTTCCATTGTTTATGGCCTAATTATTAT
         65 TGAATCGTCTTCGATTTGGCAACCCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAAT

                       *             
       3219 CATTTTGGTGATATTAGTACACTGT
        130 CATTTTGGTGAGATTAGTACACTGT

                                                                             
       3244 GAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGGGCCTATCGAGGCCCATTAGTTCCGTTTT
          1 GAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGGGCCTATCGAGGCCCATTAGTTCCGTTTT

                                                                             
       3309 GAATCGTCTTCGATTTGGCAACCCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATC
         66 GAATCGTCTTCGATTTGGCAACCCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATC

                                  * 
       3374 ATTTTGGTGAGATTAGTACACTAT
        131 ATTTTGGTGAGATTAGTACACTGT

             *                                        *  *    *      **      
       3398 GTAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGGGCCTAACGGGGCCAATTAGTGACGTTTT
          1 GAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGGGCCTATCGAGGCCCATTAGTTCCGTTTT

                                     *                        *              
       3463 GAATCGTCTTCGATTTGGCAACCCTAAATGCTTTTCTTTCCATTGTTTATTGCCTAACTATAATC
         66 GAATCGTCTTCGATTTGGCAACCCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATC

                  *                  
       3528 ATTTTGCTGAGATTAG-ACCACTGT
        131 ATTTTGGTGAGATTAGTA-CACTGT

                                                                             
       3552 GAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGGGCCTATCGAGGCCCATTAGTTCCGTTTT
          1 GAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGGGCCTATCGAGGCCCATTAGTTCCGTTTT

                   *  *                                                      
       3617 GAATCGTTTTTGATTTGGCAACCCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATC
         66 GAATCGTCTTCGATTTGGCAACCCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATC

                                  * 
       3682 ATTTTGGTGAGATTAGTACACTAT
        131 ATTTTGGTGAGATTAGTACACTGT

                                                                             
       3706 -ATAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGGGCCTATCGAGGCCCATTAGTTCCGTTT
          1 GA-AGTTTTTAGCTCATTTGGAACACTTGTTATTTTGGGCCTATCGAGGCCCATTAGTTCCGTTT

                                       *  *                       *   *   *  
       3770 TGAATCGTCTTCGATTTGGCAACCCTCTATTCTTTTCTTTCCATTGTTTATGGCTTAATTATTAT
         65 TGAATCGTCTTCGATTTGGCAACCCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAAT

                       **     *      
       3835 CATTTTGGTGATTTTAGTCCACTGT
        130 CATTTTGGTGAGATTAGTACACTGT

                                                                             
       3860 GAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGGGCCTATCGAGGCCCATTAGTTCCGTTTT
          1 GAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGGGCCTATCGAGGCCCATTAGTTCCGTTTT

                                         *     *                     *   *   
       3925 GAATCGTCTTCGATTTGGCAACCCTCAATTCTTTTATTTCCATTGTTTATGGCCTAATTATTATC
         66 GAATCGTCTTCGATTTGGCAACCCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATC

                      *      *      
       3990 ATTTTGGTGATATTAGTCCACTGT
        131 ATTTTGGTGAGATTAGTACACTGT

              *                                                              
       4014 GATGTTTTTAGCTCATTTGGAACACTTGTTATTTTGGGCCTATCGAGGCCCATTAGTTCCGTTTT
          1 GAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGGGCCTATCGAGGCCCATTAGTTCCGTTTT

                                                                             
       4079 GAATCGTCTTCGATTTGGCAACCCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATC
         66 GAATCGTCTTCGATTTGGCAACCCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATC

                                  * 
       4144 ATTTTGGTGAGATTAGTACACTAT
        131 ATTTTGGTGAGATTAGTACACTGT

             *                    *                                          
       4168 GTAGTTTTTAGCTCATTTGGAATACTTGTTATTTTGGGCCTATCGAGGCCCATTAGTTCCGTTTT
          1 GAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGGGCCTATCGAGGCCCATTAGTTCCGTTTT

                                         *                           *   *   
       4233 GAATCGTCTTCGATTTGGCAACCCTCAATTCTTTTCTTTCCATTGTTTATGGCCTAATTATTATC
         66 GAATCGTCTTCGATTTGGCAACCCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATC

                      *             
       4298 ATTTTGGTGATATTAGTACACTGT
        131 ATTTTGGTGAGATTAGTACACTGT

                                                                             
       4322 GAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGGGCCTATCGAGGCCCATTAGTTCCGTTTT
          1 GAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGGGCCTATCGAGGCCCATTAGTTCCGTTTT

                                      
       4387 GAATCGTCTTCGATTTGGCAACCCTC
         66 GAATCGTCTTCGATTTGGCAACCCTC


Statistics
Matches: 1665,  Mismatches: 102, Indels: 38
        0.92            0.06        0.02

Matches are distributed among these distances:
 152   51  0.03
 153   52  0.03
 154  1328  0.80
 155  184  0.11
 156   50  0.03

ACGTcount: A:0.21, C:0.19, G:0.18, T:0.42


Consensus pattern (154 bp):   
GAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGGGCCTATCGAGGCCCATTAGTTCCGTTTT
GAATCGTCTTCGATTTGGCAACCCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATC
ATTTTGGTGAGATTAGTACACTGT

Done.