Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01021789.1 Corchorus olitorius cultivar O-4 contig21822, 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: 18490
ACGTcount: A:0.31, C:0.19, G:0.16, T:0.33


Found at i:12912 original size:14 final size:14

Alignment explanation


    Indices: 12893--12926  Score: 68
    Period size: 14  Copynumber: 2.4  Consensus size: 14

      12883 TAAACACTCT

                          
      12893 TCTGTCGGGCCTCC
          1 TCTGTCGGGCCTCC

                          
      12907 TCTGTCGGGCCTCC
          1 TCTGTCGGGCCTCC

                  
      12921 TCTGTC
          1 TCTGTC

      12927 ATCCACTTCA


Statistics
Matches: 20,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  14   20  1.00

ACGTcount: A:0.00, C:0.41, G:0.26, T:0.32


Consensus pattern (14 bp):   
TCTGTCGGGCCTCC

Found at i:15322 original size:61 final size:61

Alignment explanation


    Indices: 15251--15375  Score: 155
    Period size: 61  Copynumber: 2.0  Consensus size: 61

      15241 GAGACTGGGC

                        * **                   *      *               *    
      15251 CCCTATCTGCTTTATTAAGGCCTA-CTGAGTAAG-TCATATATATGTCGGACACCAACTTGAA
          1 CCCTATCTGCTTCAGCAAGGCCTATC-GAGT-AGCCCATATACATGTCGGACACCAACCTGAA

                                                         *               
      15312 CCCTATCTGCTTCAGCAAGGCCTATCGAGTAGCCCATATACATGTTGGACACCAACCTGAA
          1 CCCTATCTGCTTCAGCAAGGCCTATCGAGTAGCCCATATACATGTCGGACACCAACCTGAA

               
      15373 CCC
          1 CCC

      15376 AAACGCCTAG


Statistics
Matches: 55,  Mismatches: 7, Indels: 4
        0.83            0.11        0.06

Matches are distributed among these distances:
  60    2  0.04
  61   52  0.95
  62    1  0.02

ACGTcount: A:0.28, C:0.29, G:0.17, T:0.26


Consensus pattern (61 bp):   
CCCTATCTGCTTCAGCAAGGCCTATCGAGTAGCCCATATACATGTCGGACACCAACCTGAA

Found at i:16497 original size:32 final size:32

Alignment explanation


    Indices: 16461--16524  Score: 101
    Period size: 32  Copynumber: 2.0  Consensus size: 32

      16451 CCTCCCTGCC

                            *        *      
      16461 ATTTTCTTTTGTTTTCGTTCCCAATGTTTCTT
          1 ATTTTCTTTTGTTTTCATTCCCAATATTTCTT

                                *           
      16493 ATTTTCTTTTGTTTTCATTCTCAATATTTCTT
          1 ATTTTCTTTTGTTTTCATTCCCAATATTTCTT

      16525 TTGAAGAGAG


Statistics
Matches: 29,  Mismatches: 3, Indels: 0
        0.91            0.09        0.00

Matches are distributed among these distances:
  32   29  1.00

ACGTcount: A:0.12, C:0.17, G:0.06, T:0.64


Consensus pattern (32 bp):   
ATTTTCTTTTGTTTTCATTCCCAATATTTCTT

Found at i:16923 original size:12 final size:12

Alignment explanation


    Indices: 16906--16936  Score: 53
    Period size: 12  Copynumber: 2.6  Consensus size: 12

      16896 CAGATGAAGA

                        
      16906 TTTTATTATGAT
          1 TTTTATTATGAT

                  *     
      16918 TTTTATCATGAT
          1 TTTTATTATGAT

                   
      16930 TTTTATT
          1 TTTTATT

      16937 TGAAAATTTA


Statistics
Matches: 17,  Mismatches: 2, Indels: 0
        0.89            0.11        0.00

Matches are distributed among these distances:
  12   17  1.00

ACGTcount: A:0.23, C:0.03, G:0.06, T:0.68


Consensus pattern (12 bp):   
TTTTATTATGAT
Done.