Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01009609.1 Corchorus olitorius cultivar O-4 contig09641, 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: 5815
ACGTcount: A:0.30, C:0.24, G:0.21, T:0.25


Found at i:3776 original size:33 final size:33

Alignment explanation


    Indices: 3739--3926  Score: 184
    Period size: 33  Copynumber: 5.7  Consensus size: 33

       3729 CGATCTCCGC

                  *  *                 *     
       3739 TCCAATTGCAATCAGCAGCTTCACAGCCACAGT
          1 TCCAATAGCCATCAGCAGCTTCACAGCTACAGT

                 *  *            *       * * *
       3772 TCCAACAGTCATCAGCAGCTTTAC-GACTTCCGC
          1 TCCAATAGCCATCAGCAGCTTCACAG-CTACAGT

                  *                          
       3805 TCCAATTGCCATCAGCAGCTTCACAGCTACAGT
          1 TCCAATAGCCATCAGCAGCTTCACAGCTACAGT

                                         * *   
       3838 TCCAATAGCCATCAGCAGCTTCAC-GACTTCCGCT
          1 TCCAATAGCCATCAGCAGCTTCACAG-CTACAG-T

                  *                          
       3872 T-CAATTGCCATCAGCAGCTTCACAGCTACAGT
          1 TCCAATAGCCATCAGCAGCTTCACAGCTACAGT

             *   *     *           
       3904 TTCAACAGCCAACAGCAGCTTCA
          1 TCCAATAGCCATCAGCAGCTTCA

       3927 TGGCCTCAAT


Statistics
Matches: 124,  Mismatches: 25, Indels: 12
        0.77            0.16        0.07

Matches are distributed among these distances:
  32    4  0.03
  33  116  0.94
  34    4  0.03

ACGTcount: A:0.28, C:0.35, G:0.15, T:0.23


Consensus pattern (33 bp):   
TCCAATAGCCATCAGCAGCTTCACAGCTACAGT

Found at i:3822 original size:66 final size:66

Alignment explanation


    Indices: 3716--3926  Score: 316
    Period size: 66  Copynumber: 3.2  Consensus size: 66

       3706 TTCAGTCGCT

                  *  *                       *                 *             
       3716 ATCAGCGGCCTCACGA-TCTCCGCTCCAATTGCAATCAGCAGCTTCACAGCCACAGTTCCAACAG
          1 ATCAGCAGCTTCACGACT-TCCGCTCCAATTGCCATCAGCAGCTTCACAGCTACAGTTCCAACAG

            * 
       3780 TC
         65 CC

                       *                                                 *   
       3782 ATCAGCAGCTTTACGACTTCCGCTCCAATTGCCATCAGCAGCTTCACAGCTACAGTTCCAATAGC
          1 ATCAGCAGCTTCACGACTTCCGCTCCAATTGCCATCAGCAGCTTCACAGCTACAGTTCCAACAGC

             
       3847 C
         66 C

                                    *                                *       
       3848 ATCAGCAGCTTCACGACTTCCGCTTCAATTGCCATCAGCAGCTTCACAGCTACAGTTTCAACAGC
          1 ATCAGCAGCTTCACGACTTCCGCTCCAATTGCCATCAGCAGCTTCACAGCTACAGTTCCAACAGC

             
       3913 C
         66 C

             *           
       3914 AACAGCAGCTTCA
          1 ATCAGCAGCTTCA

       3927 TGGCCTCAAT


Statistics
Matches: 132,  Mismatches: 12, Indels: 2
        0.90            0.08        0.01

Matches are distributed among these distances:
  66  131  0.99
  67    1  0.01

ACGTcount: A:0.27, C:0.36, G:0.16, T:0.22


Consensus pattern (66 bp):   
ATCAGCAGCTTCACGACTTCCGCTCCAATTGCCATCAGCAGCTTCACAGCTACAGTTCCAACAGC
C
Done.