Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01000365.1 Corchorus olitorius cultivar O-4 contig00365, 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: 6472
ACGTcount: A:0.35, C:0.15, G:0.16, T:0.34


Found at i:237 original size:2 final size:2

Alignment explanation


    Indices: 230--257  Score: 56
    Period size: 2  Copynumber: 14.0  Consensus size: 2

        220 CTAGAATGGA

                                                     
        230 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
          1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT

        258 CTTTCAAAGG


Statistics
Matches: 26,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   26  1.00

ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50


Consensus pattern (2 bp):   
AT

Found at i:2920 original size:31 final size:31

Alignment explanation


    Indices: 2822--2926  Score: 147
    Period size: 31  Copynumber: 3.4  Consensus size: 31

       2812 CCGGTATCCG

                                           
       2822 ACGTGGCATGCCATGTGTACCAAAAAGCGAC
          1 ACGTGGCATGCCATGTGTACCAAAAAGCGAC

             *   *  *    *            *    
       2853 ATGTGACACGCCACGTGTACCAAAAAACGAC
          1 ACGTGGCATGCCATGTGTACCAAAAAGCGAC

                          *            *   
       2884 ACGTGGCATGCCATATGTACCAAAAAGTGAC
          1 ACGTGGCATGCCATGTGTACCAAAAAGCGAC

                        
       2915 ACGTGGCATGCC
          1 ACGTGGCATGCC

       2927 TCGTGCACAA


Statistics
Matches: 62,  Mismatches: 12, Indels: 0
        0.84            0.16        0.00

Matches are distributed among these distances:
  31   62  1.00

ACGTcount: A:0.33, C:0.27, G:0.24, T:0.16


Consensus pattern (31 bp):   
ACGTGGCATGCCATGTGTACCAAAAAGCGAC

Found at i:6334 original size:20 final size:19

Alignment explanation


    Indices: 6320--6356  Score: 67
    Period size: 19  Copynumber: 2.0  Consensus size: 19

       6310 ATTTATCTTG

                               
       6320 AAATGGGTAGTTTTATTTA
          1 AAATGGGTAGTTTTATTTA

                               
       6339 AAATGGGTAGTTTT-TTTA
          1 AAATGGGTAGTTTTATTTA

       6357 TTTTGTTTTG


Statistics
Matches: 18,  Mismatches: 0, Indels: 1
        0.95            0.00        0.05

Matches are distributed among these distances:
  18    4  0.22
  19   14  0.78

ACGTcount: A:0.30, C:0.00, G:0.22, T:0.49


Consensus pattern (19 bp):   
AAATGGGTAGTTTTATTTA

Found at i:6449 original size:2 final size:2

Alignment explanation


    Indices: 6437--6472  Score: 63
    Period size: 2  Copynumber: 18.0  Consensus size: 2

       6427 TTATAATTAG

                  *                                              
       6437 TA TA GA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
          1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA


Statistics
Matches: 32,  Mismatches: 2, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
   2   32  1.00

ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47


Consensus pattern (2 bp):   
TA

Done.