Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01001316.1 Corchorus olitorius cultivar O-4 contig01316, 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, 828

Length: 1380
ACGTcount: A:0.32, C:0.21, G:0.13, T:0.35


Found at i:525 original size:21 final size:21

Alignment explanation


    Indices: 457--639  Score: 147
    Period size: 22  Copynumber: 8.4  Consensus size: 21

        447 TGAATTTTTT

                            *     
        457 TATGAAATTTTGATAATTACCC
          1 TATGAAATTTTGATAACTA-CC

               *                  
        479 TATTAAATTTTGATAACTACCC
          1 TATGAAATTTTGATAACTA-CC

                                 
        501 TATGAAATTTTGATAACTACC
          1 TATGAAATTTTGATAACTACC

                     *            
        522 TATGAAATTGTGATAAACT-CC
          1 TATGAAATTTTGAT-AACTACC

                    *            * 
        543 ATATGAAACTTTGATAACATAGC
          1 -TATGAAATTTTGATAAC-TACC

               *       *        *  
        566 TATAAAATTTTAATAAACCTTCC
          1 TATGAAATTTTGAT-AA-CTACC

                               ** 
        589 TATGAAATTTTG-TAACCTTTC
          1 TATGAAATTTTGATAA-CTACC

                  *            *  
        610 TATG-AGTTTTGATAACCTCCC
          1 TATGAAATTTTGATAA-CTACC

               *     
        631 TATAAAATT
          1 TATGAAATT

        640 ATATATCGTT


Statistics
Matches: 133,  Mismatches: 20, Indels: 16
        0.79            0.12        0.09

Matches are distributed among these distances:
  20    6  0.05
  21   41  0.31
  22   70  0.53
  23   15  0.11
  24    1  0.01

ACGTcount: A:0.37, C:0.15, G:0.09, T:0.39


Consensus pattern (21 bp):   
TATGAAATTTTGATAACTACC

Found at i:574 original size:65 final size:66

Alignment explanation


    Indices: 457--597  Score: 155
    Period size: 65  Copynumber: 2.1  Consensus size: 66

        447 TGAATTTTTT

                     *               *   *                 *       *         
        457 TATGAAATTTTGATAATTACCCTATTAAATTTTGATAACTACCCTATGAAATTTTGAT-AA-CTA
          1 TATGAAATTGTGATAA-TACCCTATGAAACTTTGATAACTACCCTATAAAATTTTAATAAACCTA

              
        520 CC
         65 CC

                                                        *                    
        522 TATGAAATTGTGATAA-ACTCCATATGAAACTTTGATAACATA-GCTATAAAATTTTAATAAACC
          1 TATGAAATTGTGATAATAC-CC-TATGAAACTTTGATAAC-TACCCTATAAAATTTTAATAAACC

             *  
        585 TTCC
         63 TACC

                     
        589 TATGAAATT
          1 TATGAAATT

        598 TTGTAACCTT


Statistics
Matches: 64,  Mismatches: 7, Indels: 8
        0.81            0.09        0.10

Matches are distributed among these distances:
  63    2  0.03
  64    2  0.03
  65   43  0.67
  66    4  0.06
  67   13  0.20

ACGTcount: A:0.40, C:0.14, G:0.09, T:0.38


Consensus pattern (66 bp):   
TATGAAATTGTGATAATACCCTATGAAACTTTGATAACTACCCTATAAAATTTTAATAAACCTAC
C
Done.