Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01020327.1 Corchorus olitorius cultivar O-4 contig20360, 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: 23670
ACGTcount: A:0.32, C:0.16, G:0.18, T:0.34


Found at i:9 original size:2 final size:2

Alignment explanation


    Indices: 3--43  Score: 82
    Period size: 2  Copynumber: 20.5  Consensus size: 2

          1 TG

                                                                         
          3 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
          1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T

         44 GAGTATACAT


Statistics
Matches: 39,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   39  1.00

ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51


Consensus pattern (2 bp):   
TA

Found at i:1486 original size:13 final size:13

Alignment explanation


    Indices: 1468--1492  Score: 50
    Period size: 13  Copynumber: 1.9  Consensus size: 13

       1458 TTAGAATTTC

                         
       1468 AAATAATATTTAT
          1 AAATAATATTTAT

                        
       1481 AAATAATATTTA
          1 AAATAATATTTA

       1493 CAAAATTAAA


Statistics
Matches: 12,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  13   12  1.00

ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44


Consensus pattern (13 bp):   
AAATAATATTTAT

Found at i:4846 original size:19 final size:19

Alignment explanation


    Indices: 4822--4889  Score: 77
    Period size: 19  Copynumber: 3.7  Consensus size: 19

       4812 GCGGTACAGA

                               
       4822 ACAGATGAGATTACACTGT
          1 ACAGATGAGATTACACTGT

                  *            
       4841 ACAGATAAGATTACACTGT
          1 ACAGATGAGATTACACTGT

              **    *          
       4860 --TTATGATATTACACTGT
          1 ACAGATGAGATTACACTGT

               *         
       4877 ACATATGAGATTA
          1 ACAGATGAGATTA

       4890 TTATAATAGA


Statistics
Matches: 40,  Mismatches: 7, Indels: 4
        0.78            0.14        0.08

Matches are distributed among these distances:
  17   13  0.32
  19   27  0.68

ACGTcount: A:0.38, C:0.13, G:0.16, T:0.32


Consensus pattern (19 bp):   
ACAGATGAGATTACACTGT

Found at i:11676 original size:30 final size:30

Alignment explanation


    Indices: 11613--11682  Score: 81
    Period size: 30  Copynumber: 2.3  Consensus size: 30

      11603 GCCCGTATTA

                  *           *           
      11613 TATATAAATAATATAATATAATGAAATAAT
          1 TATATATATAATATAATAAAATGAAATAAT

                 *                          
      11643 TATATTTATAA-ATAATAAAATTG-AATAATT
          1 TATATATATAATATAATAAAA-TGAAATAA-T

                      
      11673 TATATATATA
          1 TATATATATA

      11683 CATCAATTAG


Statistics
Matches: 34,  Mismatches: 4, Indels: 4
        0.81            0.10        0.10

Matches are distributed among these distances:
  29   13  0.38
  30   21  0.62

ACGTcount: A:0.56, C:0.00, G:0.03, T:0.41


Consensus pattern (30 bp):   
TATATATATAATATAATAAAATGAAATAAT

Found at i:11827 original size:25 final size:24

Alignment explanation


    Indices: 11782--11828  Score: 60
    Period size: 25  Copynumber: 1.9  Consensus size: 24

      11772 TTAATGTTTA

                           *        
      11782 AATTTTATTTTTTATTAAAAATTT
          1 AATTTTATTTTTTATAAAAAATTT

                                    
      11806 AATTATTATTTATTT-TAAAAAAT
          1 AATT-TTATTT-TTTATAAAAAAT

      11829 AAATATGGGT


Statistics
Matches: 20,  Mismatches: 1, Indels: 3
        0.83            0.04        0.12

Matches are distributed among these distances:
  24    4  0.20
  25   13  0.65
  26    3  0.15

ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57


Consensus pattern (24 bp):   
AATTTTATTTTTTATAAAAAATTT
Done.