Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01009658.1 Corchorus olitorius cultivar O-4 contig09690, 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: 5772
ACGTcount: A:0.30, C:0.17, G:0.19, T:0.34


Found at i:727 original size:169 final size:169

Alignment explanation


    Indices: 430--789  Score: 428
    Period size: 169  Copynumber: 2.1  Consensus size: 169

        420 ATTATTTACA

                                   *                   *                     
        430 ACTTTCATGAAGGACTCAAAAGCTAATTTTTATATTTCGAGTCTAAAAAATGCTTTCGAAATTTG
          1 ACTTTCATGAAGGACTCAAAAGCCAATTTTTATATTTCGAGTCAAAAAAATGCTTTCGAAATTTG

                                                      *             *        
        495 GCGGTTTCAATTAACGCTCTATTTAAAATGATATATAATTTTTGATCCAGCTGTCCGATTAAAGT
         66 GCGGTTTCAATTAACGCTCTATTTAAAATGATATATAATTTTCGATCCAGCTGTCCAATTAAAGT

                                    *             *
        560 TATTCAAGTGCCGATCAAAAGATTGTTCCATGATCTACT
        131 TATTCAAGTGCCGATCAAAAGATTATTCCATGATCTACG

                                              *                              
        599 ACTTTCATGAAGGACTCAAAAGCCAATTTTTAATGTTTCGTA-TCAAAAAAACTGC-TTCTGAAA
          1 ACTTTCATGAAGGACTCAAAAGCCAATTTTT-ATATTTCG-AGTCAAAAAAA-TGCTTTC-GAAA

                 *      *    *   *         *          *                      
        662 TTT-GTGGTTTCGATT-GCTGGTCTATTT-ATAT-ATCATATCATTTTCGATCCA-CATGTCCAA
         62 TTTGGCGGTTTCAATTAAC-GCTCTATTTAAAATGAT-ATATAATTTTCGATCCAGC-TGTCCAA

                       *     *    *     *     *           
        722 TTAAAGTTATTTAAGTGTCGATTAAAAGGTTATTGCATGATCTACG
        124 TTAAAGTTATTCAAGTGCCGATCAAAAGATTATTCCATGATCTACG

                       *     *    
        768 ACTTTCATGAACGACTCGAAAG
          1 ACTTTCATGAAGGACTCAAAAG

        790 TTAAATTTCA


Statistics
Matches: 164,  Mismatches: 20, Indels: 14
        0.83            0.10        0.07

Matches are distributed among these distances:
 168    3  0.02
 169  114  0.70
 170   36  0.22
 171   11  0.07

ACGTcount: A:0.32, C:0.16, G:0.15, T:0.37


Consensus pattern (169 bp):   
ACTTTCATGAAGGACTCAAAAGCCAATTTTTATATTTCGAGTCAAAAAAATGCTTTCGAAATTTG
GCGGTTTCAATTAACGCTCTATTTAAAATGATATATAATTTTCGATCCAGCTGTCCAATTAAAGT
TATTCAAGTGCCGATCAAAAGATTATTCCATGATCTACG

Found at i:4437 original size:18 final size:18

Alignment explanation


    Indices: 4414--4448  Score: 52
    Period size: 18  Copynumber: 1.9  Consensus size: 18

       4404 GCAATCTGAT

                              
       4414 TTTGTCAGAGGTGATGAC
          1 TTTGTCAGAGGTGATGAC

                  * *        
       4432 TTTGTCGGTGGTGATGA
          1 TTTGTCAGAGGTGATGA

       4449 TATGCCGGAG


Statistics
Matches: 15,  Mismatches: 2, Indels: 0
        0.88            0.12        0.00

Matches are distributed among these distances:
  18   15  1.00

ACGTcount: A:0.17, C:0.09, G:0.37, T:0.37


Consensus pattern (18 bp):   
TTTGTCAGAGGTGATGAC
Done.