Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01004947.1 Corchorus olitorius cultivar O-4 contig04966, 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, 758

Length: 1264
ACGTcount: A:0.38, C:0.14, G:0.17, T:0.31


Found at i:227 original size:26 final size:25

Alignment explanation


    Indices: 152--240  Score: 79
    Period size: 26  Copynumber: 3.4  Consensus size: 25

        142 TTTAAATTTT

                                       
        152 AGAGAATGGAGTAATGCCAAAAAAAAA
          1 AGAGAATGGAGTAATGCC--AAAAAAA

                    *   *   ***    ** 
        179 AGAGAATGAAGGAAATTTTAAAAGTA
          1 AGAGAATGGA-GTAATGCCAAAAAAA

                                     
        205 AGAGAATGGAGTAATGCCAAAAAAA
          1 AGAGAATGGAGTAATGCCAAAAAAA

                       
        230 ATGAGAATGGA
          1 A-GAGAATGGA

        241 TGAAGTTTTA


Statistics
Matches: 46,  Mismatches: 14, Indels: 5
        0.71            0.22        0.08

Matches are distributed among these distances:
  25   10  0.22
  26   23  0.50
  27    9  0.20
  28    4  0.09

ACGTcount: A:0.55, C:0.04, G:0.25, T:0.16


Consensus pattern (25 bp):   
AGAGAATGGAGTAATGCCAAAAAAA

Found at i:250 original size:52 final size:53

Alignment explanation


    Indices: 152--257  Score: 169
    Period size: 52  Copynumber: 2.0  Consensus size: 53

        142 TTTAAATTTT

                                                                 
        152 AGAGAATGGAGTAATGCCAAAAAAAAAAGAGAATGAAGGAAATTTTAAAAGTA
          1 AGAGAATGGAGTAATGCCAAAAAAAAAAGAGAATGAAGGAAATTTTAAAAGTA

                                       *       * *   *           
        205 AGAGAATGGAGTAATGCC-AAAAAAAATGAGAATGGATGAAGTTTTAAAAGTA
          1 AGAGAATGGAGTAATGCCAAAAAAAAAAGAGAATGAAGGAAATTTTAAAAGTA

             
        257 A
          1 A

        258 AATGACTCAT


Statistics
Matches: 49,  Mismatches: 4, Indels: 1
        0.91            0.07        0.02

Matches are distributed among these distances:
  52   31  0.63
  53   18  0.37

ACGTcount: A:0.54, C:0.04, G:0.24, T:0.19


Consensus pattern (53 bp):   
AGAGAATGGAGTAATGCCAAAAAAAAAAGAGAATGAAGGAAATTTTAAAAGTA
Done.