Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01008202.1 Corchorus capsularis cultivar CVL-1 contig08223, 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: 19276
ACGTcount: A:0.29, C:0.19, G:0.19, T:0.32


Found at i:15838 original size:6 final size:6

Alignment explanation


    Indices: 15829--15874  Score: 83
    Period size: 6  Copynumber: 7.5  Consensus size: 6

      15819 AAAGCAAAGC

                                                                 
      15829 AAATCT AAATCT AAATCT AAATCT AAATCT AAATCT AAAATCT AAA
          1 AAATCT AAATCT AAATCT AAATCT AAATCT AAATCT -AAATCT AAA

      15875 GTAAATTAAT


Statistics
Matches: 39,  Mismatches: 0, Indels: 2
        0.95            0.00        0.05

Matches are distributed among these distances:
   6   33  0.85
   7    6  0.15

ACGTcount: A:0.54, C:0.15, G:0.00, T:0.30


Consensus pattern (6 bp):   
AAATCT

Found at i:15887 original size:13 final size:13

Alignment explanation


    Indices: 15871--15905  Score: 61
    Period size: 13  Copynumber: 2.7  Consensus size: 13

      15861 ATCTAAAATC

                         
      15871 TAAAGTAAATTAA
          1 TAAAGTAAATTAA

                 *       
      15884 TAAAGCAAATTAA
          1 TAAAGTAAATTAA

                     
      15897 TAAAGTAAA
          1 TAAAGTAAA

      15906 CAATAATTAT


Statistics
Matches: 20,  Mismatches: 2, Indels: 0
        0.91            0.09        0.00

Matches are distributed among these distances:
  13   20  1.00

ACGTcount: A:0.63, C:0.03, G:0.09, T:0.26


Consensus pattern (13 bp):   
TAAAGTAAATTAA

Found at i:19038 original size:21 final size:21

Alignment explanation


    Indices: 18990--19076  Score: 58
    Period size: 21  Copynumber: 4.1  Consensus size: 21

      18980 TTGTGACTTG

                                  *
      18990 GGATGGCGCGGCATAGGCT-CGT
          1 GGATGGCGCGGCAT-GG-TGCGC

                                 
      19012 GG-TGGCGCGGCATGGTGCGC
          1 GGATGGCGCGGCATGGTGCGC

                   **    *       
      19032 GGATGGCTTGGCAAGG-GC-C
          1 GGATGGCGCGGCATGGTGCGC

                                    
      19051 GGGCATGGC-CGAGCATGGTGCGC
          1 -GG-ATGGCGCG-GCATGGTGCGC

               
      19074 GGA
          1 GGA

      19077 CATAGCTGGG


Statistics
Matches: 52,  Mismatches: 6, Indels: 15
        0.71            0.08        0.21

Matches are distributed among these distances:
  19    2  0.04
  20   11  0.21
  21   32  0.62
  22    6  0.12
  23    1  0.02

ACGTcount: A:0.13, C:0.23, G:0.49, T:0.15


Consensus pattern (21 bp):   
GGATGGCGCGGCATGGTGCGC
Done.