Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01011315.1 Corchorus olitorius cultivar O-4 contig11348, 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: 2723
ACGTcount: A:0.29, C:0.17, G:0.18, T:0.36


Found at i:221 original size:79 final size:79

Alignment explanation


    Indices: 89--238  Score: 246
    Period size: 79  Copynumber: 1.9  Consensus size: 79

         79 TTGGACAATG

                                                  *                       *  
         89 ACTCTGAATCTGATGTTGTAACTGAAAACTTCTTGATTGATGATGAAAAAGGACCAATGTGCGGT
          1 ACTCTGAATCTGATGTTGTAACTGAAAACTTCTTGATTAATGATGAAAAAGGACCAATGTGCAGT

                          
        154 CAACTTGAAAAATA
         66 CAACTTGAAAAATA

                   *                   **                   *                
        168 ACTCTGAGTCTGATGTTGTAACTGAAAGTTTCTTGATTAATGATGAAAGAGGACCAATGTGCAGT
          1 ACTCTGAATCTGATGTTGTAACTGAAAACTTCTTGATTAATGATGAAAAAGGACCAATGTGCAGT

                  
        233 CAACTT
         66 CAACTT

        239 TGATAACTTG


Statistics
Matches: 65,  Mismatches: 6, Indels: 0
        0.92            0.08        0.00

Matches are distributed among these distances:
  79   65  1.00

ACGTcount: A:0.34, C:0.14, G:0.21, T:0.31


Consensus pattern (79 bp):   
ACTCTGAATCTGATGTTGTAACTGAAAACTTCTTGATTAATGATGAAAAAGGACCAATGTGCAGT
CAACTTGAAAAATA

Found at i:831 original size:50 final size:50

Alignment explanation


    Indices: 689--834  Score: 229
    Period size: 50  Copynumber: 2.9  Consensus size: 50

        679 AATGTCCTTC

                                                *     *       
        689 GAAAAGCGAATTTTGATCTTGGACTCACAAATGGAATGCAATCTTACTTT
          1 GAAAAGCGAATTTTGATCTTGGACTCACAAATGGAAAGCAATTTTACTTT

                   *                 *   *                    
        739 GAAAAGCAAATTTTGATCTTGGACTTACACATGGAAAGCAATTTTACTTT
          1 GAAAAGCGAATTTTGATCTTGGACTCACAAATGGAAAGCAATTTTACTTT

                                 *     *                  
        789 GAAAAGCGAATTTTGATCTTGAACTCATAAATGGAAAGCAATTTTA
          1 GAAAAGCGAATTTTGATCTTGGACTCACAAATGGAAAGCAATTTTA

        835 TTGTAAAACT


Statistics
Matches: 86,  Mismatches: 10, Indels: 0
        0.90            0.10        0.00

Matches are distributed among these distances:
  50   86  1.00

ACGTcount: A:0.37, C:0.14, G:0.17, T:0.32


Consensus pattern (50 bp):   
GAAAAGCGAATTTTGATCTTGGACTCACAAATGGAAAGCAATTTTACTTT

Found at i:1472 original size:26 final size:24

Alignment explanation


    Indices: 1431--1495  Score: 85
    Period size: 26  Copynumber: 2.6  Consensus size: 24

       1421 ATTCATTCTC

                *                   
       1431 TTTTGATTTTGATTTGATTTGATT
          1 TTTTAATTTTGATTTGATTTGATT

                                      
       1455 TTTTAATTATTGACTTTGATTTGATT
          1 TTTTAATT-TTGA-TTTGATTTGATT

               * *         
       1481 TTTGATTTTTGATTT
          1 TTTTAATTTTGATTT

       1496 TTTTTCTTTT


Statistics
Matches: 36,  Mismatches: 3, Indels: 4
        0.84            0.07        0.09

Matches are distributed among these distances:
  24   10  0.28
  25    8  0.22
  26   18  0.50

ACGTcount: A:0.18, C:0.02, G:0.14, T:0.66


Consensus pattern (24 bp):   
TTTTAATTTTGATTTGATTTGATT
Done.