Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01017686.1 Corchorus olitorius cultivar O-4 contig17719, 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: 14540
ACGTcount: A:0.32, C:0.20, G:0.20, T:0.27


Found at i:2671 original size:37 final size:37

Alignment explanation


    Indices: 2629--2755  Score: 202
    Period size: 37  Copynumber: 3.4  Consensus size: 37

       2619 TCCAAAGTGA

                     *       *                   
       2629 AACAAGTCTTCATCAAAATTATTCATCAAAGTTCTTC
          1 AACAAGTCTCCATCAAAGTTATTCATCAAAGTTCTTC

                                                  
       2666 AACAAGTCTCCA-CGAAAGTTATTCATCAAAGTTCTTC
          1 AACAAGTCTCCATC-AAAGTTATTCATCAAAGTTCTTC

                        *                        
       2703 AACAAGTCTCCACCAAAGTTATTCATCAAAGTTCTTC
          1 AACAAGTCTCCATCAAAGTTATTCATCAAAGTTCTTC

                     *      
       2740 AACAAGTCTTCATCAA
          1 AACAAGTCTCCATCAA

       2756 GTTGTTCTTC


Statistics
Matches: 84,  Mismatches: 4, Indels: 4
        0.91            0.04        0.04

Matches are distributed among these distances:
  36    1  0.01
  37   82  0.98
  38    1  0.01

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


Consensus pattern (37 bp):   
AACAAGTCTCCATCAAAGTTATTCATCAAAGTTCTTC

Found at i:2755 original size:24 final size:24

Alignment explanation


    Indices: 2650--2789  Score: 92
    Period size: 24  Copynumber: 5.7  Consensus size: 24

       2640 ATCAAAATTA

                                    
       2650 TTCATCAAAGTTCTTCAACAAGTC
          1 TTCATCAAAGTTCTTCAACAAGTC

             *           *    *        
       2674 TCCA-CGAAAGTTATTCATCAAAGTTC
          1 TTCATC-AAAGTTCTTCAAC-AAG-TC

                *         *  *       *
       2700 TTCAAC-AAG-TCTCCACCAAAGTTA
          1 TTCATCAAAGTTCTTCAAC-AAG-TC

                                    
       2724 TTCATCAAAGTTCTTCAACAAGTC
          1 TTCATCAAAGTTCTTCAACAAGTC

                      *              *
       2748 TTCATCAAGTTGTTCTTCAACAAGTT
          1 TTCATCAA--AGTTCTTCAACAAGTC

                              
       2774 TTCACTC--AGTTCTTCA
          1 TTCA-TCAAAGTTCTTCA

       2790 TCAAATTTTC


Statistics
Matches: 92,  Mismatches: 15, Indels: 19
        0.73            0.12        0.15

Matches are distributed among these distances:
  23    9  0.10
  24   39  0.42
  25   12  0.13
  26   29  0.32
  27    3  0.03

ACGTcount: A:0.31, C:0.25, G:0.09, T:0.34


Consensus pattern (24 bp):   
TTCATCAAAGTTCTTCAACAAGTC

Found at i:2793 original size:26 final size:26

Alignment explanation


    Indices: 2738--2793  Score: 69
    Period size: 26  Copynumber: 2.2  Consensus size: 26

       2728 TCAAAGTTCT

                                 *   *
       2738 TCAACAAGTCTTCATCAAGTTGTTCT
          1 TCAACAAGTCTTCATCAAGTTCTTCA

                     *                 
       2764 TCAACAAGTTTTCACTC-AGTTCTTCA
          1 TCAACAAGTCTTCA-TCAAGTTCTTCA

                
       2790 TCAA
          1 TCAA

       2794 ATTTTCCACC


Statistics
Matches: 26,  Mismatches: 3, Indels: 2
        0.84            0.10        0.06

Matches are distributed among these distances:
  26   24  0.92
  27    2  0.08

ACGTcount: A:0.29, C:0.25, G:0.09, T:0.38


Consensus pattern (26 bp):   
TCAACAAGTCTTCATCAAGTTCTTCA

Found at i:10724 original size:52 final size:52

Alignment explanation


    Indices: 10644--10796  Score: 254
    Period size: 52  Copynumber: 3.0  Consensus size: 52

      10634 TAAAAAAAAT

                                                                
      10644 GCCTGCTAAGTTGAAAACCCCATTGGGGCGGCTTAGGCAAAAGTTAAGGCAA
          1 GCCTGCTAAGTTGAAAACCCCATTGGGGCGGCTTAGGCAAAAGTTAAGGCAA

                                   *                            
      10696 GCCTGCTAAGTTGAAAACCCCATCGGGGCGGCTTAGGCAAAAGTTAAGGCAA
          1 GCCTGCTAAGTTGAAAACCCCATTGGGGCGGCTTAGGCAAAAGTTAAGGCAA

             *      *                    *  *                 
      10748 GACTGCTAGGTTGAAAACCCCATTGGGGCAGCCTAGGCAAAAG-TAAGGC
          1 GCCTGCTAAGTTGAAAACCCCATTGGGGCGGCTTAGGCAAAAGTTAAGGC

      10797 TTAAAAAAAA


Statistics
Matches: 95,  Mismatches: 6, Indels: 1
        0.93            0.06        0.01

Matches are distributed among these distances:
  51    6  0.06
  52   89  0.94

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


Consensus pattern (52 bp):   
GCCTGCTAAGTTGAAAACCCCATTGGGGCGGCTTAGGCAAAAGTTAAGGCAA

Found at i:14505 original size:44 final size:44

Alignment explanation


    Indices: 14398--14540  Score: 216
    Period size: 44  Copynumber: 3.2  Consensus size: 44

      14388 GAGAAGGTCG

                 *  *                                    
      14398 AAGAGGCCAATGCAGAGGTAGAGGGCGATGAAAATCAACCCCGCC
          1 AAGAGTCCGATGCAGAGGTAGAGGGCGATGAAAATCAACCCCG-C

                                                        
      14443 AAGAGTCCGATGCAGAGGTAGAGGGCGATGAAAATCAACCCCGC
          1 AAGAGTCCGATGCAGAGGTAGAGGGCGATGAAAATCAACCCCGC

                   *                 **                  
      14487 AAGAGTCTGATGCAGAGGTAGAGGGTAAT-AAACATCAACCCCGC
          1 AAGAGTCCGATGCAGAGGTAGAGGGCGATGAAA-ATCAACCCCGC

                      
      14531 AAGAGTCCGA
          1 AAGAGTCCGA


Statistics
Matches: 91,  Mismatches: 6, Indels: 3
        0.91            0.06        0.03

Matches are distributed among these distances:
  43    3  0.03
  44   47  0.52
  45   41  0.45

ACGTcount: A:0.36, C:0.22, G:0.30, T:0.12


Consensus pattern (44 bp):   
AAGAGTCCGATGCAGAGGTAGAGGGCGATGAAAATCAACCCCGC
Done.