Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01019046.1 Corchorus olitorius cultivar O-4 contig19079, 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: 7328
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33


Found at i:1716 original size:28 final size:28

Alignment explanation


    Indices: 1676--1734  Score: 118
    Period size: 28  Copynumber: 2.1  Consensus size: 28

       1666 ATACTGTGAA

                                        
       1676 AAAGTGTGGTAGAAAAGTAAAATGACCT
          1 AAAGTGTGGTAGAAAAGTAAAATGACCT

                                        
       1704 AAAGTGTGGTAGAAAAGTAAAATGACCT
          1 AAAGTGTGGTAGAAAAGTAAAATGACCT

               
       1732 AAA
          1 AAA

       1735 ATGATATAAA


Statistics
Matches: 31,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  28   31  1.00

ACGTcount: A:0.49, C:0.07, G:0.24, T:0.20


Consensus pattern (28 bp):   
AAAGTGTGGTAGAAAAGTAAAATGACCT

Found at i:2963 original size:13 final size:13

Alignment explanation


    Indices: 2945--2971  Score: 54
    Period size: 13  Copynumber: 2.1  Consensus size: 13

       2935 TAATTTATAT

                         
       2945 TATAGTTTATACG
          1 TATAGTTTATACG

                         
       2958 TATAGTTTATACG
          1 TATAGTTTATACG

             
       2971 T
          1 T

       2972 TTGACAGAGA


Statistics
Matches: 14,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  13   14  1.00

ACGTcount: A:0.30, C:0.07, G:0.15, T:0.48


Consensus pattern (13 bp):   
TATAGTTTATACG

Found at i:5508 original size:28 final size:28

Alignment explanation


    Indices: 5468--5563  Score: 108
    Period size: 28  Copynumber: 3.5  Consensus size: 28

       5458 ATTTACTTCT

                                     *  
       5468 CATTTTGATCATTTTGCATGTCCAGAGG
          1 CATTTTGATCATTTTGCATGTCCAGGGG

                                         
       5496 CATTTTGATCATTTTGCATG-CCTAGGGG
          1 CATTTTGATCATTTTGCATGTCC-AGGGG

            *                  **        
       5524 TATTTT-AGTCA-TTTGCACATCCAGGGG
          1 CATTTTGA-TCATTTTGCATGTCCAGGGG

                   *     
       5551 CATTTTGGTCATT
          1 CATTTTGATCATT

       5564 GCAAGTACAT


Statistics
Matches: 57,  Mismatches: 6, Indels: 10
        0.78            0.08        0.14

Matches are distributed among these distances:
  27   22  0.39
  28   35  0.61

ACGTcount: A:0.20, C:0.18, G:0.22, T:0.41


Consensus pattern (28 bp):   
CATTTTGATCATTTTGCATGTCCAGGGG
Done.