Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01015950.1 Corchorus capsularis cultivar CVL-1 contig15971, 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: 5040
ACGTcount: A:0.34, C:0.14, G:0.21, T:0.31


Found at i:2873 original size:17 final size:17

Alignment explanation


    Indices: 2851--2883  Score: 57
    Period size: 17  Copynumber: 1.9  Consensus size: 17

       2841 AATGAAAAGG

                     *       
       2851 TTGTTTTTGGAATAAAA
          1 TTGTTTTTGAAATAAAA

                            
       2868 TTGTTTTTGAAATAAA
          1 TTGTTTTTGAAATAAA

       2884 GGGATAGTTT


Statistics
Matches: 15,  Mismatches: 1, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
  17   15  1.00

ACGTcount: A:0.36, C:0.00, G:0.15, T:0.48


Consensus pattern (17 bp):   
TTGTTTTTGAAATAAAA

Found at i:3834 original size:16 final size:16

Alignment explanation


    Indices: 3801--3834  Score: 50
    Period size: 16  Copynumber: 2.1  Consensus size: 16

       3791 AGTTCAAATC

                        **  
       3801 AAAAGAAAAGAATTGA
          1 AAAAGAAAAGAAAAGA

                            
       3817 AAAAGAAAAGAAAAGA
          1 AAAAGAAAAGAAAAGA

              
       3833 AA
          1 AA

       3835 GAAGTTGAAA


Statistics
Matches: 16,  Mismatches: 2, Indels: 0
        0.89            0.11        0.00

Matches are distributed among these distances:
  16   16  1.00

ACGTcount: A:0.76, C:0.00, G:0.18, T:0.06


Consensus pattern (16 bp):   
AAAAGAAAAGAAAAGA

Found at i:4116 original size:36 final size:37

Alignment explanation


    Indices: 4047--4116  Score: 97
    Period size: 36  Copynumber: 1.9  Consensus size: 37

       4037 TTAAAGTGTG

                     *                 **        
       4047 ATCTTTTCACAAGAAAAAATGTTTTCCTCAAAGTGCA
          1 ATCTTTTCAAAAGAAAAAATGTTTTCCAAAAAGTGCA

                                     *        
       4084 ATCTTTTCAAAAG-AAAAATGTTTTTCAAAAAGT
          1 ATCTTTTCAAAAGAAAAAATGTTTTCCAAAAAGT

       4117 TTTTAAGACA


Statistics
Matches: 29,  Mismatches: 4, Indels: 1
        0.85            0.12        0.03

Matches are distributed among these distances:
  36   17  0.59
  37   12  0.41

ACGTcount: A:0.41, C:0.14, G:0.10, T:0.34


Consensus pattern (37 bp):   
ATCTTTTCAAAAGAAAAAATGTTTTCCAAAAAGTGCA
Done.