Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01004307.1 Corchorus olitorius cultivar O-4 contig04320, 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, 631

Length: 1052
ACGTcount: A:0.32, C:0.12, G:0.24, T:0.33


Found at i:54 original size:19 final size:20

Alignment explanation


    Indices: 19--57  Score: 62
    Period size: 19  Copynumber: 2.0  Consensus size: 20

          9 ATGAGCTTTG

                      *         
         19 ACAAATGAAATTTGGGTATT
          1 ACAAATGAAAGTTGGGTATT

                                
         39 ACAAAT-AAAGTTGGGTATT
          1 ACAAATGAAAGTTGGGTATT

         58 GTAGATAGCC


Statistics
Matches: 18,  Mismatches: 1, Indels: 1
        0.90            0.05        0.05

Matches are distributed among these distances:
  19   12  0.67
  20    6  0.33

ACGTcount: A:0.41, C:0.05, G:0.21, T:0.33


Consensus pattern (20 bp):   
ACAAATGAAAGTTGGGTATT

Found at i:147 original size:16 final size:16

Alignment explanation


    Indices: 112--161  Score: 52
    Period size: 15  Copynumber: 3.2  Consensus size: 16

        102 TTTGAAGGCT

                         *  
        112 AAGAA-AAA-GAAGGA
          1 AAGAAGAAAGGAAAGA

                            
        126 AA-AAGAAAGGAAAGA
          1 AAGAAGAAAGGAAAGA

                              
        141 AAGAAGAAAGTGAAAGGA
          1 AAGAAGAAAG-GAAA-GA

               
        159 AAG
          1 AAG

        162 GGAGAGGGGG


Statistics
Matches: 30,  Mismatches: 1, Indels: 6
        0.81            0.03        0.16

Matches are distributed among these distances:
  13    2  0.07
  14    5  0.17
  15    7  0.23
  16    7  0.23
  17    4  0.13
  18    5  0.17

ACGTcount: A:0.68, C:0.00, G:0.30, T:0.02


Consensus pattern (16 bp):   
AAGAAGAAAGGAAAGA
Done.