Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01023847.1 Corchorus olitorius cultivar O-4 contig23880, 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: 1712
ACGTcount: A:0.35, C:0.20, G:0.15, T:0.30


Found at i:681 original size:43 final size:43

Alignment explanation


    Indices: 630--782  Score: 270
    Period size: 43  Copynumber: 3.6  Consensus size: 43

        620 TAATATATGA

                                                       
        630 ATTTAAAATATCTTTCCATAATTTAAAAATAGAATTATGGTGG
          1 ATTTAAAATATCTTTCCATAATTTAAAAATAGAATTATGGTGG

               *                                      *
        673 ATTCAAAATATCTTTCCATAATTTAAAAATAGAATTATGGTGA
          1 ATTTAAAATATCTTTCCATAATTTAAAAATAGAATTATGGTGG

                        *                     *        
        716 ATTTAAAATATCGTTCCATAATTTAAAAATAGAAGTATGGTGG
          1 ATTTAAAATATCTTTCCATAATTTAAAAATAGAATTATGGTGG

                                    
        759 ATTTAAAATATCTTTCCATAATTT
          1 ATTTAAAATATCTTTCCATAATTT

        783 CTTTTTGGCC


Statistics
Matches: 103,  Mismatches: 7, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
  43  103  1.00

ACGTcount: A:0.42, C:0.08, G:0.10, T:0.39


Consensus pattern (43 bp):   
ATTTAAAATATCTTTCCATAATTTAAAAATAGAATTATGGTGG

Found at i:703 original size:21 final size:21

Alignment explanation


    Indices: 677--746  Score: 54
    Period size: 21  Copynumber: 3.3  Consensus size: 21

        667 TGGTGGATTC

                                 
        677 AAAATATCTTTCCATAATTTA
          1 AAAATATCTTTCCATAATTTA

                   **     **        
        698 AAAATAGAATTAT-GGTGAATTT-
          1 AAAATA-TCTT-TCCAT-AATTTA

                    *            
        720 AAAATATCGTTCCATAATTTA
          1 AAAATATCTTTCCATAATTTA

                  
        741 AAAATA
          1 AAAATA

        747 GAAGTATGGT


Statistics
Matches: 35,  Mismatches: 9, Indels: 10
        0.65            0.17        0.19

Matches are distributed among these distances:
  20    6  0.17
  21   14  0.40
  22    9  0.26
  23    6  0.17

ACGTcount: A:0.47, C:0.09, G:0.07, T:0.37


Consensus pattern (21 bp):   
AAAATATCTTTCCATAATTTA
Done.