Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01006148.1 Corchorus olitorius cultivar O-4 contig06173, 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: 1750
ACGTcount: A:0.31, C:0.22, G:0.19, T:0.28


Found at i:782 original size:13 final size:13

Alignment explanation


    Indices: 762--845  Score: 86
    Period size: 13  Copynumber: 6.8  Consensus size: 13

        752 GTGAAACAAG

                         
        762 TCTTCATCAAAGT
          1 TCTTCATCAAAGT

             *           
        775 TATTCATCAAAGT
          1 TCTTCATCAAAGT

                  *      
        788 TCTTCAAC-AAG-
          1 TCTTCATCAAAGT

               *  *      
        799 TCTCCACCAAAGT
          1 TCTTCATCAAAGT

             *           
        812 TATTCATCAAAGT
          1 TCTTCATCAAAGT

                  *      
        825 TCTTCAAC-AAG-
          1 TCTTCATCAAAGT

                      
        836 TCTTCATCAA
          1 TCTTCATCAA

        846 GTTGTTCTTC


Statistics
Matches: 57,  Mismatches: 11, Indels: 7
        0.76            0.15        0.09

Matches are distributed among these distances:
  11   13  0.23
  12   10  0.18
  13   34  0.60

ACGTcount: A:0.35, C:0.25, G:0.07, T:0.33


Consensus pattern (13 bp):   
TCTTCATCAAAGT

Found at i:797 original size:37 final size:37

Alignment explanation


    Indices: 756--845  Score: 162
    Period size: 37  Copynumber: 2.4  Consensus size: 37

        746 CCAAGAGTGA

                                                 
        756 AACAAGTCTTCATCAAAGTTATTCATCAAAGTTCTTC
          1 AACAAGTCTTCATCAAAGTTATTCATCAAAGTTCTTC

                     *  *                        
        793 AACAAGTCTCCACCAAAGTTATTCATCAAAGTTCTTC
          1 AACAAGTCTTCATCAAAGTTATTCATCAAAGTTCTTC

                            
        830 AACAAGTCTTCATCAA
          1 AACAAGTCTTCATCAA

        846 GTTGTTCTTC


Statistics
Matches: 49,  Mismatches: 4, Indels: 0
        0.92            0.08        0.00

Matches are distributed among these distances:
  37   49  1.00

ACGTcount: A:0.37, C:0.24, G:0.08, T:0.31


Consensus pattern (37 bp):   
AACAAGTCTTCATCAAAGTTATTCATCAAAGTTCTTC

Found at i:883 original size:26 final size:26

Alignment explanation


    Indices: 823--883  Score: 70
    Period size: 26  Copynumber: 2.3  Consensus size: 26

        813 ATTCATCAAA

                *                     
        823 GTTCTTCAACAAGTCTTCATCAAGTT
          1 GTTCATCAACAAGTCTTCATCAAGTT

                *         *            
        849 GTTCTTCAACAAGTTTTCACTC-AGTT
          1 GTTCATCAACAAGTCTTCA-TCAAGTT

            *        
        875 TTTCATCAA
          1 GTTCATCAA

        884 ATTTTCCACC


Statistics
Matches: 31,  Mismatches: 3, Indels: 2
        0.86            0.08        0.06

Matches are distributed among these distances:
  26   29  0.94
  27    2  0.06

ACGTcount: A:0.26, C:0.23, G:0.10, T:0.41


Consensus pattern (26 bp):   
GTTCATCAACAAGTCTTCATCAAGTT

Found at i:1673 original size:52 final size:52

Alignment explanation


    Indices: 1590--1739  Score: 248
    Period size: 52  Copynumber: 2.9  Consensus size: 52

       1580 AAAAAATGCA

                                            *                   
       1590 TGCTAAGTTGAAAACCCCATTGGGGCGGCTTAAGCAAAAGTTAAGGCAAGCC
          1 TGCTAAGTTGAAAACCCCATTGGGGCGGCTTAGGCAAAAGTTAAGGCAAGCC

                                *     *                         
       1642 TGCTAAGTTGAAAACCCCATCGGGGCAGCTTAGGCAAAAGTTAAGGCAAGCC
          1 TGCTAAGTTGAAAACCCCATTGGGGCGGCTTAGGCAAAAGTTAAGGCAAGCC

                 *                       *                 
       1694 TGCTAGGTTGAAAACCCCATTGGGGCGGCCTAGGCAAAAG-TAAGGC
          1 TGCTAAGTTGAAAACCCCATTGGGGCGGCTTAGGCAAAAGTTAAGGC

       1740 TAAAAAAAAA


Statistics
Matches: 91,  Mismatches: 7, Indels: 1
        0.92            0.07        0.01

Matches are distributed among these distances:
  51    6  0.07
  52   85  0.93

ACGTcount: A:0.31, C:0.22, G:0.29, T:0.18


Consensus pattern (52 bp):   
TGCTAAGTTGAAAACCCCATTGGGGCGGCTTAGGCAAAAGTTAAGGCAAGCC
Done.