Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01021785.1 Corchorus olitorius cultivar O-4 contig21818, 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: 10038
ACGTcount: A:0.33, C:0.20, G:0.16, T:0.31


Found at i:5704 original size:12 final size:11

Alignment explanation


    Indices: 5687--5734  Score: 69
    Period size: 12  Copynumber: 4.2  Consensus size: 11

       5677 TTAATTCACT

                       
       5687 TTTGATTTGAA
          1 TTTGATTTGAA

                     *  
       5698 CTTTGATTTTAA
          1 -TTTGATTTGAA

                        
       5710 TTTCGATTTGAA
          1 TTT-GATTTGAA

                       
       5722 TTTGATTTGAA
          1 TTTGATTTGAA

              
       5733 TT
          1 TT

       5735 ACTTAACGAA


Statistics
Matches: 33,  Mismatches: 2, Indels: 3
        0.87            0.05        0.08

Matches are distributed among these distances:
  11   13  0.39
  12   20  0.61

ACGTcount: A:0.25, C:0.04, G:0.15, T:0.56


Consensus pattern (11 bp):   
TTTGATTTGAA

Found at i:6071 original size:15 final size:14

Alignment explanation


    Indices: 6019--6077  Score: 77
    Period size: 14  Copynumber: 4.3  Consensus size: 14

       6009 TAAAAGACTC

                          
       6019 AAAACC-TTT-TTG
          1 AAAACCTTTTCTTG

                      *   
       6031 AAAACCTTTTTTTG
          1 AAAACCTTTTCTTG

                          
       6045 AAAACCTTTTCTTG
          1 AAAACCTTTTCTTG

                  *        
       6059 AAAACAATTTTCTTG
          1 AAAAC-CTTTTCTTG

                
       6074 AAAA
          1 AAAA

       6078 TCATGTATTG


Statistics
Matches: 42,  Mismatches: 2, Indels: 3
        0.89            0.04        0.06

Matches are distributed among these distances:
  12    6  0.14
  13    3  0.07
  14   21  0.50
  15   12  0.29

ACGTcount: A:0.37, C:0.15, G:0.07, T:0.41


Consensus pattern (14 bp):   
AAAACCTTTTCTTG

Found at i:9980 original size:41 final size:41

Alignment explanation


    Indices: 9935--10038  Score: 138
    Period size: 41  Copynumber: 2.5  Consensus size: 41

       9925 AAATAAATCT

                 *                *            *      
       9935 TAAATCAGGGACAAAATTGAATCAATAAATAAATATTA-CTC
          1 TAAATTAGGGACAAAATTGAATAAATAAATAAATAATAGC-C

                                          *          
       9976 TAAATTAGGGACAAAATTGAATAAATAAATCAATAATAGCC
          1 TAAATTAGGGACAAAATTGAATAAATAAATAAATAATAGCC

                        **        
      10017 TAAATTAGGGACCCAATTGAAT
          1 TAAATTAGGGACAAAATTGAAT


Statistics
Matches: 56,  Mismatches: 6, Indels: 2
        0.88            0.09        0.03

Matches are distributed among these distances:
  41   55  0.98
  42    1  0.02

ACGTcount: A:0.50, C:0.12, G:0.12, T:0.26


Consensus pattern (41 bp):   
TAAATTAGGGACAAAATTGAATAAATAAATAAATAATAGCC
Done.