Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01009494.1 Corchorus olitorius cultivar O-4 contig09526, 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, 649

Length: 1083
ACGTcount: A:0.34, C:0.16, G:0.14, T:0.37


Found at i:268 original size:107 final size:106

Alignment explanation


    Indices: 102--371  Score: 321
    Period size: 106  Copynumber: 2.5  Consensus size: 106

         92 TCCCTTAAAA

                *                *       *  *    * *                         
        102 TAAAATTGGGGCTAAACTTAGCG-AATTAATTATATACTGTATTTCTAAAACCCTATAACAATAA
          1 TAAATTTGGGGCTAAACTTAGTGAAATTAGTTTTATATTTTATTTCT-AAACCCTATAACAATAA

                        *           *            *     
        166 GTCATTAATTTTTAAATTTA-CCTTAACATAAAATTTTAAATT
         65 GTCATTAATTTTGAAATTTACCCTCAACATAAAA-TTAAAATT

                                      *                                      
        208 TAAATTTGGGGCTAAACTTAGTGAAAATAGTTTTATATTTTATTTCTATAACCCTATAACAATAA
          1 TAAATTTGGGGCTAAACTTAGTGAAATTAGTTTTATATTTTATTTCTA-AACCCTATAACAATAA

              *          *             *              
        273 GTTATTAATTTTGGAATTTACCCTCAATATAAAATTAAAATT
         65 GTCATTAATTTTGAAATTTACCCTCAACATAAAATTAAAATT

             **      *  *       *                                     
        315 TTTATTT-GAGCAAAACTTAATGAAATTAGTTTTATATTTTATTTCTAAAGCCCTATA
          1 TAAATTTGGGGCTAAACTTAGTGAAATTAGTTTTATATTTTATTTCTAAA-CCCTATA

        372 GTAAAAAATA


Statistics
Matches: 141,  Mismatches: 19, Indels: 8
        0.84            0.11        0.05

Matches are distributed among these distances:
 105    2  0.01
 106   65  0.46
 107   63  0.45
 108   11  0.08

ACGTcount: A:0.39, C:0.11, G:0.09, T:0.41


Consensus pattern (106 bp):   
TAAATTTGGGGCTAAACTTAGTGAAATTAGTTTTATATTTTATTTCTAAACCCTATAACAATAAG
TCATTAATTTTGAAATTTACCCTCAACATAAAATTAAAATT

Found at i:731 original size:26 final size:25

Alignment explanation


    Indices: 701--752  Score: 68
    Period size: 26  Copynumber: 2.0  Consensus size: 25

        691 AGGTCGCGAC

                    *   *             
        701 GCGGGTCGTGCGTGACCCTAGCCATG
          1 GCGGGTCGCGCGCGACCC-AGCCATG

                              *      
        727 GCGGGTCGCGCGCGACCCGGCCATG
          1 GCGGGTCGCGCGCGACCCAGCCATG

             
        752 G
          1 G

        753 ACCCGGGTCG


Statistics
Matches: 23,  Mismatches: 3, Indels: 1
        0.85            0.11        0.04

Matches are distributed among these distances:
  25    7  0.30
  26   16  0.70

ACGTcount: A:0.10, C:0.35, G:0.42, T:0.13


Consensus pattern (25 bp):   
GCGGGTCGCGCGCGACCCAGCCATG
Done.