Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01014158.1 Corchorus olitorius cultivar O-4 contig14191, 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: 14018
ACGTcount: A:0.33, C:0.18, G:0.19, T:0.31


Found at i:6766 original size:37 final size:36

Alignment explanation


    Indices: 6667--6773  Score: 111
    Period size: 37  Copynumber: 3.1  Consensus size: 36

       6657 TATGGTTTCC

                 *                               
       6667 AAATCCCAAAATGACATTGTTTGACGTAATAAGACCA
          1 AAATCTCAAAATGACA-TGTTTGACGTAATAAGACCA

                     *                        * 
       6704 AAAT-TC--TATGA-AT-TTTG--GTAATAAGACTA
          1 AAATCTCAAAATGACATGTTTGACGTAATAAGACCA

                                        *        
       6733 AAATCTCAAAATGACATCGTTTGACGTAGTAAGACCA
          1 AAATCTCAAAATGACAT-GTTTGACGTAATAAGACCA

                
       6770 AAAT
          1 AAAT

       6774 TCTGTGAGAA


Statistics
Matches: 56,  Mismatches: 6, Indels: 16
        0.72            0.08        0.21

Matches are distributed among these distances:
  29   15  0.27
  30    2  0.04
  31    4  0.07
  32    5  0.09
  33    3  0.05
  34    4  0.07
  35    4  0.07
  36    1  0.02
  37   18  0.32

ACGTcount: A:0.43, C:0.15, G:0.14, T:0.28


Consensus pattern (36 bp):   
AAATCTCAAAATGACATGTTTGACGTAATAAGACCA

Found at i:12512 original size:21 final size:21

Alignment explanation


    Indices: 12488--12542  Score: 83
    Period size: 21  Copynumber: 2.6  Consensus size: 21

      12478 GGCACTGAAT

                *             *  
      12488 GGTGATGGCACGGGCATAGCC
          1 GGTGGTGGCACGGGCATAACC

                           *     
      12509 GGTGGTGGCACGGGCTTAACC
          1 GGTGGTGGCACGGGCATAACC

                         
      12530 GGTGGTGGCACGG
          1 GGTGGTGGCACGG

      12543 AAATGGGCGG


Statistics
Matches: 31,  Mismatches: 3, Indels: 0
        0.91            0.09        0.00

Matches are distributed among these distances:
  21   31  1.00

ACGTcount: A:0.15, C:0.22, G:0.47, T:0.16


Consensus pattern (21 bp):   
GGTGGTGGCACGGGCATAACC

Done.