Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01010299.1 Corchorus capsularis cultivar CVL-1 contig10320, 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: 32687
ACGTcount: A:0.33, C:0.18, G:0.16, T:0.32

Warning! 1 characters in sequence are not A, C, G, or T


Found at i:6 original size:1 final size:1

Alignment explanation


    Indices: 1--40  Score: 71
    Period size: 1  Copynumber: 40.0  Consensus size: 1

                    *                               
          1 AAAAAAAANAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
          1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA

         41 CTGTCTACTT


Statistics
Matches: 37,  Mismatches: 2, Indels: 0
        0.95            0.05        0.00

Matches are distributed among these distances:
   1   37  1.00

ACGTcount: A:0.97, C:0.00, G:0.00, T:0.00


Consensus pattern (1 bp):   
A

Found at i:15932 original size:23 final size:23

Alignment explanation


    Indices: 15901--15950  Score: 59
    Period size: 22  Copynumber: 2.2  Consensus size: 23

      15891 ATATGTTATG

                                     
      15901 AAAATTTTAAGTTTT-AAATTTTTC
          1 AAAATTTT-A-TTTTAAAATTTTTC

                                  *
      15925 AAAA-TTTATTTTAAAATTTTTT
          1 AAAATTTTATTTTAAAATTTTTC

                
      15947 AAAA
          1 AAAA

      15951 AAAATATTTT


Statistics
Matches: 24,  Mismatches: 1, Indels: 4
        0.83            0.03        0.14

Matches are distributed among these distances:
  21    4  0.17
  22   13  0.54
  23    3  0.12
  24    4  0.17

ACGTcount: A:0.44, C:0.02, G:0.02, T:0.52


Consensus pattern (23 bp):   
AAAATTTTATTTTAAAATTTTTC

Found at i:28327 original size:17 final size:18

Alignment explanation


    Indices: 28305--28339  Score: 54
    Period size: 18  Copynumber: 2.0  Consensus size: 18

      28295 TTCCAGTTGC

                              
      28305 TTCTGGG-TCTGTGGGGT
          1 TTCTGGGCTCTGTGGGGT

                     *        
      28322 TTCTGGGCTTTGTGGGGT
          1 TTCTGGGCTCTGTGGGGT

      28340 GTGGGGGAGC


Statistics
Matches: 16,  Mismatches: 1, Indels: 1
        0.89            0.06        0.06

Matches are distributed among these distances:
  17    7  0.44
  18    9  0.56

ACGTcount: A:0.00, C:0.11, G:0.46, T:0.43


Consensus pattern (18 bp):   
TTCTGGGCTCTGTGGGGT

Done.