Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01022309.1 Corchorus olitorius cultivar O-4 contig22342, 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: 13897
ACGTcount: A:0.32, C:0.19, G:0.17, T:0.32


Found at i:4051 original size:21 final size:22

Alignment explanation


    Indices: 4012--4052  Score: 66
    Period size: 22  Copynumber: 1.9  Consensus size: 22

       4002 ACAAATTATC

                    *             
       4012 TCCTCCAATTCCGCCTGCTCTG
          1 TCCTCCAACTCCGCCTGCTCTG

                                
       4034 TCCTCCAACTCC-CCTGCTC
          1 TCCTCCAACTCCGCCTGCTC

       4053 ATCCATAATA


Statistics
Matches: 18,  Mismatches: 1, Indels: 1
        0.90            0.05        0.05

Matches are distributed among these distances:
  21    7  0.39
  22   11  0.61

ACGTcount: A:0.10, C:0.51, G:0.10, T:0.29


Consensus pattern (22 bp):   
TCCTCCAACTCCGCCTGCTCTG

Found at i:5899 original size:106 final size:106

Alignment explanation


    Indices: 5733--6014  Score: 417
    Period size: 107  Copynumber: 2.7  Consensus size: 106

       5723 TTTTTAACCT

                       * **      *                             *             
       5733 TTAAAATAAAATTTTAATTTTGATTT-GGGCTAAACTTAGTG-AATTAGTTATATATTTTATTTC
          1 TTAAAATAAAAATAAAATTTTAATTTGGGGCTAAACTTAGTGAAATTAGTTTTATATTTTATTTC

               *         *                 *         
       5796 TAACACCCTATAATAAT-ATTATTAATTATGGAATTTACCC
         66 TAAAACCCTATAACAATAATTATTAATTATGAAATTTACCC

                           *                                      *          
       5836 TTAAAATAAAAATAAGATTTTAAATTTGGGGCTAAACTTAGTGAAATTAGTTTTGTATTTTATTT
          1 TTAAAATAAAAATAAAATTTT-AATTTGGGGCTAAACTTAGTGAAATTAGTTTTATATTTTATTT

                                          *            
       5901 CTAAAACCCTATAACAATAAATTATTAATTTTGAAATTTACCC
         65 CTAAAACCCTATAACAAT-AATTATTAATTATGAAATTTACCC

                                        *                                    
       5944 TTAAAATAAAAATAAAATTTTAATTTGGAGCTAAACTTAGTGAAATTAGTTTTATATTTTATTTC
          1 TTAAAATAAAAATAAAATTTTAATTTGGGGCTAAACTTAGTGAAATTAGTTTTATATTTTATTTC

                  
       6009 TAAAAC
         66 TAAAAC

       6015 TCTAAAATAA


Statistics
Matches: 160,  Mismatches: 14, Indels: 6
        0.89            0.08        0.03

Matches are distributed among these distances:
 103   17  0.11
 104    4  0.03
 105   15  0.09
 106   35  0.22
 107   48  0.30
 108   41  0.26

ACGTcount: A:0.40, C:0.09, G:0.09, T:0.43


Consensus pattern (106 bp):   
TTAAAATAAAAATAAAATTTTAATTTGGGGCTAAACTTAGTGAAATTAGTTTTATATTTTATTTC
TAAAACCCTATAACAATAATTATTAATTATGAAATTTACCC

Found at i:13857 original size:45 final size:45

Alignment explanation


    Indices: 13808--13897  Score: 126
    Period size: 45  Copynumber: 2.0  Consensus size: 45

      13798 AATAACAATT

                                      *                  
      13808 AATATTAACTTTATCTTGATGAATTATATAGAGATGGAGAAGTAG
          1 AATATTAACTTTATCTTGATGAATTACATAGAGATGGAGAAGTAG

                   **     *            *           *     
      13853 AATATTAGTTTTATTTTGATGAATTACCTAGAGATGGAGGAGTAG
          1 AATATTAACTTTATCTTGATGAATTACATAGAGATGGAGAAGTAG


Statistics
Matches: 39,  Mismatches: 6, Indels: 0
        0.87            0.13        0.00

Matches are distributed among these distances:
  45   39  1.00

ACGTcount: A:0.37, C:0.04, G:0.22, T:0.37


Consensus pattern (45 bp):   
AATATTAACTTTATCTTGATGAATTACATAGAGATGGAGAAGTAG
Done.