Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01017254.1 Corchorus olitorius cultivar O-4 contig17287, 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: 5407
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.33


Found at i:164 original size:26 final size:29

Alignment explanation


    Indices: 117--174  Score: 68
    Period size: 26  Copynumber: 2.1  Consensus size: 29

        107 AAAAGTTTTT

                                       * 
        117 AAAAAAAAAATGAAGAGAAAAAGAAAGGG
          1 AAAAAAAAAATGAAGAGAAAAAGAAAGAG

                    *             *      
        146 AAAAAAAATAT-AAG-G-AAAATAAAGAG
          1 AAAAAAAAAATGAAGAGAAAAAGAAAGAG

               
        172 AAA
          1 AAA

        175 TTTGGAAATA


Statistics
Matches: 26,  Mismatches: 3, Indels: 3
        0.81            0.09        0.09

Matches are distributed among these distances:
  26   12  0.46
  27    1  0.04
  28    3  0.12
  29   10  0.38

ACGTcount: A:0.74, C:0.00, G:0.19, T:0.07


Consensus pattern (29 bp):   
AAAAAAAAAATGAAGAGAAAAAGAAAGAG

Found at i:3408 original size:16 final size:16

Alignment explanation


    Indices: 3387--3422  Score: 72
    Period size: 16  Copynumber: 2.2  Consensus size: 16

       3377 ATAGTAAATT

                            
       3387 TTTCTTCTATGGGTAG
          1 TTTCTTCTATGGGTAG

                            
       3403 TTTCTTCTATGGGTAG
          1 TTTCTTCTATGGGTAG

                
       3419 TTTC
          1 TTTC

       3423 GTAGTTTAGT


Statistics
Matches: 20,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  16   20  1.00

ACGTcount: A:0.11, C:0.14, G:0.22, T:0.53


Consensus pattern (16 bp):   
TTTCTTCTATGGGTAG
Done.