Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01006523.1 Corchorus olitorius cultivar O-4 contig06548, 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, 961

Length: 1603
ACGTcount: A:0.25, C:0.20, G:0.18, T:0.37


Found at i:232 original size:128 final size:128

Alignment explanation


    Indices: 1--300  Score: 494
    Period size: 128  Copynumber: 2.3  Consensus size: 128

                                                     *                       
          1 CATTTGGGGCTTTTCCATAAGCCAAGTTCGCTTCCATGCGAATATACAATTTGATTTGAAGATAG
          1 CATTTGGGGCTTTTCCATAAGCCAAGTTCGCTTCCATGCGAGTATACAATTTGATTTGAAGATAG

                                            **                            *
         66 TTCAGTCCTTCAAGACCAAACTCGTTTCCATATGAGTTAGTTTAAGCTTTGGTTCCATCCAAG
         66 TTCAGTCCTTCAAGACCAAACTCGTTTCCATACAAGTTAGTTTAAGCTTTGGTTCCATCCAAA

                                                                             
        129 CATTTGGGGCTTTTCCATAAGCCAAGTTCGCTTCCATGCGAGTATACAATTTGATTTGAAGATAG
          1 CATTTGGGGCTTTTCCATAAGCCAAGTTCGCTTCCATGCGAGTATACAATTTGATTTGAAGATAG

                   *       *                                               
        194 TTCAGTCTTTCAAGAGCAAACTCGTTTCCATACAAGTTAGTTTAAGCTTTGGTTCCATCCAAA
         66 TTCAGTCCTTCAAGACCAAACTCGTTTCCATACAAGTTAGTTTAAGCTTTGGTTCCATCCAAA

               * *                                 *     
        257 CATCTAGGGCTTTTCCATAAGCCAAAGTTCG-TCTCCATACGAGT
          1 CATTTGGGGCTTTTCCATAAGCC-AAGTTCGCT-TCCATGCGAGT

        301 CAATTCGAGC


Statistics
Matches: 161,  Mismatches: 9, Indels: 3
        0.93            0.05        0.02

Matches are distributed among these distances:
 128  144  0.89
 129   17  0.11

ACGTcount: A:0.27, C:0.22, G:0.18, T:0.34


Consensus pattern (128 bp):   
CATTTGGGGCTTTTCCATAAGCCAAGTTCGCTTCCATGCGAGTATACAATTTGATTTGAAGATAG
TTCAGTCCTTCAAGACCAAACTCGTTTCCATACAAGTTAGTTTAAGCTTTGGTTCCATCCAAA

Found at i:721 original size:53 final size:53

Alignment explanation


    Indices: 632--732  Score: 121
    Period size: 53  Copynumber: 1.9  Consensus size: 53

        622 ATCTGTGTAT

                                    **   *                       
        632 ATCTAAGCTGATTTTCTGAAGGTCTTGGGTGACCTTTCAATAAATTTTCAAAA
          1 ATCTAAGCTGATTTTCTGAAGGTCCCGGGCGACCTTTCAATAAATTTTCAAAA

                           *   **          *       * *      
        685 ATCTAAGCTGATTTTTTGATTGTCCCGGGCGGCCTTTCATTCAATTTT
          1 ATCTAAGCTGATTTTCTGAAGGTCCCGGGCGACCTTTCAATAAATTTT

        733 AGGAATCTAT


Statistics
Matches: 39,  Mismatches: 9, Indels: 0
        0.81            0.19        0.00

Matches are distributed among these distances:
  53   39  1.00

ACGTcount: A:0.24, C:0.18, G:0.18, T:0.41


Consensus pattern (53 bp):   
ATCTAAGCTGATTTTCTGAAGGTCCCGGGCGACCTTTCAATAAATTTTCAAAA

Found at i:774 original size:42 final size:43

Alignment explanation


    Indices: 727--810  Score: 118
    Period size: 43  Copynumber: 2.0  Consensus size: 43

        717 CCTTTCATTC

                                       *                
        727 AATTTTAGGA-ATCTATGTTGATTCT-TGAATCGTCTTCTTGTT
          1 AATTTTAGGAGATCTATGTTGA-TCTGCGAATCGTCTTCTTGTT

                  *                        *          
        769 AATTTTCGGAGATCTATGTTGATCTGCGAATTGTCTTCTTGT
          1 AATTTTAGGAGATCTATGTTGATCTGCGAATCGTCTTCTTGT

        811 CAACTTTCAG


Statistics
Matches: 37,  Mismatches: 3, Indels: 3
        0.86            0.07        0.07

Matches are distributed among these distances:
  42   12  0.32
  43   25  0.68

ACGTcount: A:0.20, C:0.13, G:0.19, T:0.48


Consensus pattern (43 bp):   
AATTTTAGGAGATCTATGTTGATCTGCGAATCGTCTTCTTGTT

Found at i:835 original size:43 final size:43

Alignment explanation


    Indices: 753--846  Score: 107
    Period size: 43  Copynumber: 2.2  Consensus size: 43

        743 GTTGATTCTT

                *          *  *    *          *        
        753 GAATCGTCTTCTTGTTAATTTTCGGAGATCTATGTTGATCTGC
          1 GAATTGTCTTCTTGTCAACTTTCAGAGATCTATGATGATCTGC

                                       *   *         * 
        796 GAATTGTCTTCTTGTCAACTTTCAGAGGTCTGTGATGATCTTC
          1 GAATTGTCTTCTTGTCAACTTTCAGAGATCTATGATGATCTGC

              *     
        839 GAGTTGTC
          1 GAATTGTC

        847 ATTTTAATAA


Statistics
Matches: 42,  Mismatches: 9, Indels: 0
        0.82            0.18        0.00

Matches are distributed among these distances:
  43   42  1.00

ACGTcount: A:0.18, C:0.17, G:0.22, T:0.43


Consensus pattern (43 bp):   
GAATTGTCTTCTTGTCAACTTTCAGAGATCTATGATGATCTGC

Found at i:878 original size:43 final size:43

Alignment explanation


    Indices: 831--924  Score: 118
    Period size: 43  Copynumber: 2.2  Consensus size: 43

        821 AGGTCTGTGA

                      *  *                  **       *  
        831 TGATCTTCGAGTTGTCATTTTAA-TAATATTCGGAGATCTAGGC
          1 TGATCTTCGAATTATC-TTTTAATTAATATTCAAAGATCTAAGC

                                       *               
        874 TGATCTTCGAATTATCTTTTAATTAATTTTCAAAGATCTAAGC
          1 TGATCTTCGAATTATCTTTTAATTAATATTCAAAGATCTAAGC

                    
        917 TGATCTTC
          1 TGATCTTC

        925 CAAAAAAACA


Statistics
Matches: 44,  Mismatches: 6, Indels: 2
        0.85            0.12        0.04

Matches are distributed among these distances:
  42    6  0.14
  43   38  0.86

ACGTcount: A:0.28, C:0.15, G:0.15, T:0.43


Consensus pattern (43 bp):   
TGATCTTCGAATTATCTTTTAATTAATATTCAAAGATCTAAGC
Done.