Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01000512.1 Corchorus olitorius cultivar O-4 contig00512, 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, 601

Length: 1002
ACGTcount: A:0.30, C:0.19, G:0.19, T:0.33


Found at i:830 original size:20 final size:21

Alignment explanation


    Indices: 784--837  Score: 69
    Period size: 19  Copynumber: 2.7  Consensus size: 21

        774 ATTCCAAGTG

                                 
        784 CTTTTTTTTCATTTTCTTTTT
          1 CTTTTTTTTCATTTTCTTTTT

             *                *  
        805 CATTTTTTTC-TTTTCTTCTT
          1 CTTTTTTTTCATTTTCTTTTT

                           
        825 -TTTTTTTT-ATTTT
          1 CTTTTTTTTCATTTT

        838 TTATTATTGG


Statistics
Matches: 29,  Mismatches: 3, Indels: 4
        0.81            0.08        0.11

Matches are distributed among these distances:
  19   11  0.38
  20    9  0.31
  21    9  0.31

ACGTcount: A:0.06, C:0.13, G:0.00, T:0.81


Consensus pattern (21 bp):   
CTTTTTTTTCATTTTCTTTTT

Found at i:838 original size:12 final size:12

Alignment explanation


    Indices: 785--839  Score: 56
    Period size: 12  Copynumber: 4.3  Consensus size: 12

        775 TTCCAAGTGC

                        
        785 TTTTTTTTCATT
          1 TTTTTTTTCATT

              *          
        797 TTCTTTTTCATTT
          1 TTTTTTTTCA-TT

                      *   
        810 TTTTCTTTTCTTCT
          1 TTTT-TTTTCAT-T

                    *   
        824 TTTTTTTTTATT
          1 TTTTTTTTCATT

                
        836 TTTT
          1 TTTT

        840 ATTATTGGGA


Statistics
Matches: 35,  Mismatches: 5, Indels: 6
        0.76            0.11        0.13

Matches are distributed among these distances:
  12   14  0.40
  13   11  0.31
  14   10  0.29

ACGTcount: A:0.05, C:0.11, G:0.00, T:0.84


Consensus pattern (12 bp):   
TTTTTTTTCATT

Found at i:838 original size:20 final size:18

Alignment explanation


    Indices: 785--837  Score: 61
    Period size: 20  Copynumber: 2.8  Consensus size: 18

        775 TTCCAAGTGC

                    *         
        785 TTTTTTTTCATTTTCTTT
          1 TTTTTTTTTATTTTCTTT

                       *         
        803 TTCATTTTTTTCTTTTCTTCT
          1 TT--TTTTTTTATTTTCTT-T

                          
        824 TTTTTTTTTATTTT
          1 TTTTTTTTTATTTT

        838 TTATTATTGG


Statistics
Matches: 29,  Mismatches: 3, Indels: 5
        0.78            0.08        0.14

Matches are distributed among these distances:
  18    2  0.07
  19   11  0.38
  20   13  0.45
  21    3  0.10

ACGTcount: A:0.06, C:0.11, G:0.00, T:0.83


Consensus pattern (18 bp):   
TTTTTTTTTATTTTCTTT
Done.