Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01001493.1 Corchorus capsularis cultivar CVL-1 contig01493, 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: 4098
ACGTcount: A:0.36, C:0.21, G:0.16, T:0.26


Found at i:3080 original size:76 final size:76

Alignment explanation


    Indices: 2981--3132  Score: 304
    Period size: 76  Copynumber: 2.0  Consensus size: 76

       2971 TCCTTGACAG

                                                                             
       2981 CCTCAGGAACCTTTGTGGTCTTTGGCTTTGAATCCAGAGACAAATTCTCCAGTGAATCTGCAACT
          1 CCTCAGGAACCTTTGTGGTCTTTGGCTTTGAATCCAGAGACAAATTCTCCAGTGAATCTGCAACT

                       
       3046 TCTGCGAGTGT
         66 TCTGCGAGTGT

                                                                             
       3057 CCTCAGGAACCTTTGTGGTCTTTGGCTTTGAATCCAGAGACAAATTCTCCAGTGAATCTGCAACT
          1 CCTCAGGAACCTTTGTGGTCTTTGGCTTTGAATCCAGAGACAAATTCTCCAGTGAATCTGCAACT

                       
       3122 TCTGCGAGTGT
         66 TCTGCGAGTGT

       3133 AGAAGTAAAG


Statistics
Matches: 76,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  76   76  1.00

ACGTcount: A:0.22, C:0.24, G:0.22, T:0.32


Consensus pattern (76 bp):   
CCTCAGGAACCTTTGTGGTCTTTGGCTTTGAATCCAGAGACAAATTCTCCAGTGAATCTGCAACT
TCTGCGAGTGT

Found at i:3903 original size:21 final size:21

Alignment explanation


    Indices: 3879--3936  Score: 61
    Period size: 21  Copynumber: 2.9  Consensus size: 21

       3869 TATTAGATAG

                            *    
       3879 AGAGAGAGAAGGAGAAGGAGA
          1 AGAGAGAGAAGGAGAAAGAGA

                                  
       3900 AGAG-GTAGAAGGAGAAAGAGA
          1 AGAGAG-AGAAGGAGAAAGAGA

                      *        
       3921 A-AGA-AGAAAGA-AAAGA
          1 AGAGAGAGAAGGAGAAAGA

       3937 AAACCCTATG


Statistics
Matches: 33,  Mismatches: 2, Indels: 7
        0.79            0.05        0.17

Matches are distributed among these distances:
  18    5  0.15
  19    6  0.18
  20    3  0.09
  21   19  0.58

ACGTcount: A:0.59, C:0.00, G:0.40, T:0.02


Consensus pattern (21 bp):   
AGAGAGAGAAGGAGAAAGAGA
Done.