Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01010209.1 Corchorus olitorius cultivar O-4 contig10241, 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: 3075
ACGTcount: A:0.33, C:0.18, G:0.19, T:0.29


Found at i:75 original size:27 final size:27

Alignment explanation


    Indices: 1--85  Score: 98
    Period size: 27  Copynumber: 3.0  Consensus size: 27

                                        *  
          1 TCCACTGCTGGGGGTCGAAGTGGGAGGATCC
          1 TCCACTGCT-GGGGTCGAA--GGGA-GAGCC

            * *         *              
         32 ACTACTGCTGGGATCGAAGGGAGAGCC
          1 TCCACTGCTGGGGTCGAAGGGAGAGCC

                                       
         59 TCCACTGCTGGGGTCGAAGGGAGAGCC
          1 TCCACTGCTGGGGTCGAAGGGAGAGCC

         86 GGACCAGCAA


Statistics
Matches: 47,  Mismatches: 7, Indels: 4
        0.81            0.12        0.07

Matches are distributed among these distances:
  27   28  0.60
  28    4  0.09
  30    8  0.17
  31    7  0.15

ACGTcount: A:0.20, C:0.24, G:0.40, T:0.16


Consensus pattern (27 bp):   
TCCACTGCTGGGGTCGAAGGGAGAGCC

Found at i:2051 original size:164 final size:161

Alignment explanation


    Indices: 1715--2054  Score: 382
    Period size: 164  Copynumber: 2.1  Consensus size: 161

       1705 TCTGTTGAGA

                               *          *               *                  
       1715 AAAACGCCGCTATATATTATAGGCGTAGAGTTGGAAAATTACTTTGTTTTAGGGAGAGGGAATTT
          1 AAAACGCCGCTATATATTACAGGCGTAGAGCTGGAAAATTACTTTGCTTTAGGGAGAGGGAATTT

                       *                             *      *              * 
       1780 TTCCCTCCAAACAAAGAAAAAAAATCTCTCCCTCCATATATTAATAAATAGCGGCGTTTACTGCT
         66 TTCCCTCCAAAAAAAGAAAAAAAATCTCTCCCTCCATATATCAAT-AACAGCGGCGTTTACTGAT

             * *                            
       1845 CTAGACGCCACAAATTAACGGCGTCTTGTTTT
        130 CAAAACGCCACAAATTAACGGCGTCTTGTTTT

                                   **           **  *              *         
       1877 AAAACGCCGCTATATATTACAGGTTTAGAGCTGGAAGCTTTCTTTGCTTTAGTGGGGAGGGAATT
          1 AAAACGCCGCTATATATTACAGGCGTAGAGCTGGAAAATTACTTTGCTTTAG-GGAGAGGGAATT

                                                     *          *          * 
       1942 TTTCCCTCCAAAAAAAGGAGAAAAAAAATCTCTCCCTCCATGTATCAAT-ACGGCGGCGTCTTTC
         65 TTTCCCTCC-AAAAAA--AGAAAAAAAATCTCTCCCTCCATATATCAATAACAGCGGCGT-TTAC

                         *        *               
       2006 T-ATCAAAACGCCGCTAAATT-GCGGCGTCTCT-TTTT
        126 TGATCAAAACGCCAC-AAATTAACGGCGTCT-TGTTTT

            * *           
       2041 CAGACGCCGCTATA
          1 AAAACGCCGCTATA

       2055 GCAAATTTCA


Statistics
Matches: 149,  Mismatches: 22, Indels: 12
        0.81            0.12        0.07

Matches are distributed among these distances:
 162   44  0.30
 163   20  0.13
 164   46  0.31
 165   10  0.07
 166   29  0.19

ACGTcount: A:0.30, C:0.21, G:0.19, T:0.29


Consensus pattern (161 bp):   
AAAACGCCGCTATATATTACAGGCGTAGAGCTGGAAAATTACTTTGCTTTAGGGAGAGGGAATTT
TTCCCTCCAAAAAAAGAAAAAAAATCTCTCCCTCCATATATCAATAACAGCGGCGTTTACTGATC
AAAACGCCACAAATTAACGGCGTCTTGTTTT
Done.