Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01024340.1 Corchorus olitorius cultivar O-4 contig24373, 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: 16337
ACGTcount: A:0.30, C:0.19, G:0.20, T:0.31


Found at i:1603 original size:17 final size:17

Alignment explanation


    Indices: 1583--1618  Score: 54
    Period size: 17  Copynumber: 2.1  Consensus size: 17

       1573 ATATAAAGAG

                             
       1583 CTATCTAGTATAACAAA
          1 CTATCTAGTATAACAAA

                  *  *       
       1600 CTATCTGGTGTAACAAA
          1 CTATCTAGTATAACAAA

              
       1617 CT
          1 CT

       1619 TTATAAATCA


Statistics
Matches: 17,  Mismatches: 2, Indels: 0
        0.89            0.11        0.00

Matches are distributed among these distances:
  17   17  1.00

ACGTcount: A:0.39, C:0.19, G:0.11, T:0.31


Consensus pattern (17 bp):   
CTATCTAGTATAACAAA

Found at i:3436 original size:18 final size:18

Alignment explanation


    Indices: 3373--3436  Score: 56
    Period size: 18  Copynumber: 3.6  Consensus size: 18

       3363 ATTTGAGGAT

                    *         
       3373 TGCGGCAGCGGAACATCC
          1 TGCGGCAGTGGAACATCC

                   ** *     * 
       3391 TGCGGCAAAGCAACATTC
          1 TGCGGCAGTGGAACATCC

              ** *            
       3409 TGTAGTAGTGGAACATCC
          1 TGCGGCAGTGGAACATCC

                      
       3427 TGCGGCAGTG
          1 TGCGGCAGTG

       3437 AATCAATATT


Statistics
Matches: 32,  Mismatches: 14, Indels: 0
        0.70            0.30        0.00

Matches are distributed among these distances:
  18   32  1.00

ACGTcount: A:0.25, C:0.25, G:0.31, T:0.19


Consensus pattern (18 bp):   
TGCGGCAGTGGAACATCC

Found at i:5952 original size:17 final size:17

Alignment explanation


    Indices: 5930--5965  Score: 54
    Period size: 17  Copynumber: 2.1  Consensus size: 17

       5920 ATACAAAGAG

                             
       5930 CTATCTAGTATAACAAA
          1 CTATCTAGTATAACAAA

                  *  *       
       5947 CTATCTGGTGTAACAAA
          1 CTATCTAGTATAACAAA

              
       5964 CT
          1 CT

       5966 TTACAAATCA


Statistics
Matches: 17,  Mismatches: 2, Indels: 0
        0.89            0.11        0.00

Matches are distributed among these distances:
  17   17  1.00

ACGTcount: A:0.39, C:0.19, G:0.11, T:0.31


Consensus pattern (17 bp):   
CTATCTAGTATAACAAA

Found at i:12062 original size:76 final size:76

Alignment explanation


    Indices: 11933--12083  Score: 180
    Period size: 76  Copynumber: 2.0  Consensus size: 76

      11923 TGATGAGCTA

                        *      *                                             
      11933 TGACACAGCCCATCTGGGTGATCAAGCGAAACACATGGGTCTTCAGACAAACCATGTGGGCACCC
          1 TGACACAGCCCACCTGGGTCATCAAGCGAAACACATGGGTCTTCAGACAAACCATGTGGGCACCC

                       
      11998 AACTGGAGTCG
         66 AACTGGAGTCG

                  *             *            *       *      *              * 
      12009 TGACACCGCCCACCTGGGTCCTCAAGC-AAACCGCATGGGTGTTCAAGGC-AACCATGTGGGCGC
          1 TGACACAGCCCACCTGGGTCATCAAGCGAAA-CACATGGGTCTTC-AGACAAACCATGTGGGCAC

               **       
      12072 CCAGGTGGAGTC
         64 CCAACTGGAGTC

      12084 AGGGCCCTTA


Statistics
Matches: 63,  Mismatches: 10, Indels: 4
        0.82            0.13        0.05

Matches are distributed among these distances:
  75    3  0.05
  76   57  0.90
  77    3  0.05

ACGTcount: A:0.25, C:0.30, G:0.28, T:0.17


Consensus pattern (76 bp):   
TGACACAGCCCACCTGGGTCATCAAGCGAAACACATGGGTCTTCAGACAAACCATGTGGGCACCC
AACTGGAGTCG
Done.