Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01009938.1 Corchorus capsularis cultivar CVL-1 contig09959, 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: 11285
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34


Found at i:2125 original size:213 final size:217

Alignment explanation


    Indices: 1733--2172  Score: 574
    Period size: 213  Copynumber: 2.0  Consensus size: 217

       1723 CGGAGGGAGT

                                                                     *       
       1733 ATTAAAAATCTTACTTAAAAAAATTAAAAATATCTTTAATTTCCTTGTATACAACTAGCAATTGG
          1 ATTAAAAATCTTACTTAAAAAAATTAAAAATATCTTTAATTTCCTTGTATACAACTAACAATTGG

               *  *                       *   *         **                  *
       1798 TTAGTTTAAATGGTTCGCACCCATTCTACTGAAAGATATATTCTTGGGACCGAACTTGTGAAAGG
         66 TTAATTCAAATGGTTCGCA--CA-TCTA-TAAAAAATATATTCTCAGGACCGAACTTGTGAAAGA

                       *              *                                      
       1863 AGAAAATTATTGTTCAGAGAATTTCATCCTCATGATAGACCAACCCAATTTGAACCGTTACTTTA
        127 AGAAAATTATTATTCAGAGAATTTCACCCTCATGATAGACCAACCCAATTTGAACCGTTACTTTA

                           **          
       1928 AACTTAATA-ATAT-GTATAATAGGTA
        192 AACTTAATATATATAAAAT-ATAGGTA

                                        *   *                                
       1953 ATTAAAAATCTTACTTTAAAAAAATTAATAATCTCTTTAATTTCCTTGTATACAACTAACAATTG
          1 ATTAAAAATCTTAC-TTAAAAAAATTAAAAATATCTTTAATTTCCTTGTATACAACTAACAATTG

                                                          **                 
       2018 GTTAATTCAAATGG-TC-CA-A-CT-TAAAAAATATGA-TCTCAGGTTCGAA-TATCGTGAAAGA
         65 GTTAATTCAAATGGTTCGCACATCTATAAAAAATAT-ATTCTCAGGACCGAACT-T-GTGAAAGA

                                                               *   *         
       2076 AGAAAATTATTATTCAGAGAATTTCACCCTCATGATAGACCAACCCAATTTTAACGGTTACTTTA
        127 AGAAAATTATTATTCAGAGAATTTCACCCTCATGATAGACCAACCCAATTTGAACCGTTACTTTA

                                      
       2141 AACTTAATATATATAAAATATAGGTA
        192 AACTTAATATATATAAAATATAGGTA

                  
       2167 ATTAAA
          1 ATTAAA

       2173 TCCTTATCAT


Statistics
Matches: 196,  Mismatches: 18, Indels: 18
        0.84            0.08        0.08

Matches are distributed among these distances:
 211    1  0.01
 212   18  0.09
 213   78  0.40
 214   19  0.10
 215    2  0.01
 216    1  0.01
 219    2  0.01
 220   16  0.08
 221   59  0.30

ACGTcount: A:0.40, C:0.15, G:0.11, T:0.34


Consensus pattern (217 bp):   
ATTAAAAATCTTACTTAAAAAAATTAAAAATATCTTTAATTTCCTTGTATACAACTAACAATTGG
TTAATTCAAATGGTTCGCACATCTATAAAAAATATATTCTCAGGACCGAACTTGTGAAAGAAGAA
AATTATTATTCAGAGAATTTCACCCTCATGATAGACCAACCCAATTTGAACCGTTACTTTAAACT
TAATATATATAAAATATAGGTA
Done.