Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01022053.1 Corchorus olitorius cultivar O-4 contig22086, 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: 1960
ACGTcount: A:0.29, C:0.20, G:0.22, T:0.30


Found at i:458 original size:30 final size:30

Alignment explanation


    Indices: 422--478  Score: 78
    Period size: 30  Copynumber: 1.9  Consensus size: 30

        412 GTTTGGATAA

                        *    *            
        422 TCCCAAAAGAAGGTTTTTGAAAATAAAGGT
          1 TCCCAAAAGAAGATTTTGGAAAATAAAGGT

                     *            *    
        452 TCCCAAAAGGAGATTTTGGAAATTAAA
          1 TCCCAAAAGAAGATTTTGGAAAATAAA

        479 TGGGTAAGTT


Statistics
Matches: 23,  Mismatches: 4, Indels: 0
        0.85            0.15        0.00

Matches are distributed among these distances:
  30   23  1.00

ACGTcount: A:0.44, C:0.11, G:0.19, T:0.26


Consensus pattern (30 bp):   
TCCCAAAAGAAGATTTTGGAAAATAAAGGT

Found at i:1889 original size:2 final size:2

Alignment explanation


    Indices: 1882--1923  Score: 84
    Period size: 2  Copynumber: 21.0  Consensus size: 2

       1872 GGGCCTTTGT

                                                                          
       1882 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
          1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA

       1924 TATATATATA


Statistics
Matches: 40,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   40  1.00

ACGTcount: A:0.50, C:0.50, G:0.00, T:0.00


Consensus pattern (2 bp):   
CA

Found at i:1928 original size:2 final size:2

Alignment explanation


    Indices: 1923--1955  Score: 66
    Period size: 2  Copynumber: 16.5  Consensus size: 2

       1913 ACACACACAC

                                                             
       1923 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
          1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A

       1956 GTAGT


Statistics
Matches: 31,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   31  1.00

ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48


Consensus pattern (2 bp):   
AT

Done.