Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01024028.1 Corchorus olitorius cultivar O-4 contig24061, 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: 3258
ACGTcount: A:0.34, C:0.21, G:0.18, T:0.28


Found at i:978 original size:68 final size:68

Alignment explanation


    Indices: 878--1378  Score: 797
    Period size: 68  Copynumber: 7.4  Consensus size: 68

        868 AGTCAGACCC

                                       * *         *                         
        878 GTTAAGCCTTGGTTCCATCCAAGCAGCGGGGGCTTTCTCGCAAGCCAAACTCGTTTCCATACGAG
          1 GTTAAGCCTTGGTTCCATCCAAGCAGCAGAGGCTTTCTCACAAGCCAAACTCGTTTCCATACGAG

               
        943 CCA
         66 CCA

                                     *   *         *                         
        946 GTTAAGCCTTGGTTCCATCCAAGCAACAGGGGCTTTCTCGCAAGCCAAACTCGTTTCCATACGAG
          1 GTTAAGCCTTGGTTCCATCCAAGCAGCAGAGGCTTTCTCACAAGCCAAACTCGTTTCCATACGAG

             * 
       1011 CTA
         66 CCA

                                                                             
       1014 GTTAAGCCTTGGTTCCATCCAAGCAGCAGAGGCTTTCTCACAAGCCAAACTCGTTTCCATACGAG
          1 GTTAAGCCTTGGTTCCATCCAAGCAGCAGAGGCTTTCTCACAAGCCAAACTCGTTTCCATACGAG

               
       1079 CCA
         66 CCA

                  *                                 *   *    *               
       1082 GTTAAGTCTTGGTTCCATCCAAGCAGCAGAGGCTTTCTCATAAGTCAAATTCGTTTCCATACGAG
          1 GTTAAGCCTTGGTTCCATCCAAGCAGCAGAGGCTTTCTCACAAGCCAAACTCGTTTCCATACGAG

            *  
       1147 TCA
         66 CCA

                  *                                *                         
       1150 GTTAAGTCTTGGTTCCATCCAAGCAGCAGAGGCTTTCTCGCAAGCCAAACTCGTTTCCATACGAG
          1 GTTAAGCCTTGGTTCCATCCAAGCAGCAGAGGCTTTCTCACAAGCCAAACTCGTTTCCATACGAG

               
       1215 CCA
         66 CCA

                                           *                              *  
       1218 GTTAAGCCTTGGTTCCATCCAAGCAGCAGAGACTTTCTCACAAGCCAAACTCGTTTCCATACAAG
          1 GTTAAGCCTTGGTTCCATCCAAGCAGCAGAGGCTTTCTCACAAGCCAAACTCGTTTCCATACGAG

            *  
       1283 TCA
         66 CCA

               *                         *                                   
       1286 GTTTAGCCTTGGTTCCATCCAAGCAGCAGGGGCTTT-TCCACAAGCCAAACTCGTTTCCATACGA
          1 GTTAAGCCTTGGTTCCATCCAAGCAGCAGAGGCTTTCT-CACAAGCCAAACTCGTTTCCATACGA

             *  
       1350 GTCA
         65 GCCA

               *                     
       1354 GTTTAGCCTTGGTTCCATCCAAGCA
          1 GTTAAGCCTTGGTTCCATCCAAGCA

       1379 TTCATGGGCT


Statistics
Matches: 406,  Mismatches: 26, Indels: 2
        0.94            0.06        0.00

Matches are distributed among these distances:
  67    1  0.00
  68  405  1.00

ACGTcount: A:0.25, C:0.29, G:0.20, T:0.26


Consensus pattern (68 bp):   
GTTAAGCCTTGGTTCCATCCAAGCAGCAGAGGCTTTCTCACAAGCCAAACTCGTTTCCATACGAG
CCA

Found at i:1682 original size:3 final size:3

Alignment explanation


    Indices: 1664--1696  Score: 50
    Period size: 3  Copynumber: 11.3  Consensus size: 3

       1654 AATATGTCCT

                 *                                       
       1664 AGA AAA AGA A-A AGA AGA AGA AGA AGA AGA AGA A
          1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA A

       1697 AAGGGGTTTA


Statistics
Matches: 27,  Mismatches: 2, Indels: 2
        0.87            0.06        0.06

Matches are distributed among these distances:
   2    2  0.07
   3   25  0.93

ACGTcount: A:0.73, C:0.00, G:0.27, T:0.00


Consensus pattern (3 bp):   
AGA

Done.