Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01022755.1 Corchorus olitorius cultivar O-4 contig22788, 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: 3768
ACGTcount: A:0.32, C:0.14, G:0.17, T:0.36


Found at i:1052 original size:45 final size:45

Alignment explanation


    Indices: 998--1101  Score: 129
    Period size: 45  Copynumber: 2.3  Consensus size: 45

        988 AGGCAGCCTC

                                  *    *  *       **      
        998 TTATTTTGTATAGGTC-CTTAATTTGCCATTATCTAGACGAGGCAT
          1 TTATTTTGTATAGGTCAC-TAACTTGCAATGATCTAGAAAAGGCAT

                         *                             * 
       1043 TTATTTTGTATAGATCACTAACTTGCAATGATCTAGAAAAGGCCT
          1 TTATTTTGTATAGGTCACTAACTTGCAATGATCTAGAAAAGGCAT

                          
       1088 TTATTTTGTATAGG
          1 TTATTTTGTATAGG

       1102 GTTTAGTTTT


Statistics
Matches: 50,  Mismatches: 8, Indels: 2
        0.83            0.13        0.03

Matches are distributed among these distances:
  45   49  0.98
  46    1  0.02

ACGTcount: A:0.28, C:0.13, G:0.17, T:0.41


Consensus pattern (45 bp):   
TTATTTTGTATAGGTCACTAACTTGCAATGATCTAGAAAAGGCAT

Found at i:2222 original size:28 final size:27

Alignment explanation


    Indices: 2178--2235  Score: 71
    Period size: 28  Copynumber: 2.1  Consensus size: 27

       2168 AGGAAGATTC

                     *  *       *    * 
       2178 GAGGAAGAAGGAGAAGAAAAGAGAAGA
          1 GAGGAAGAAAGAAAAGAAAAAAGAAAA

                                        
       2205 GAGGAAAGAAAGAAAAGAAAAAAGAAAA
          1 GAGG-AAGAAAGAAAAGAAAAAAGAAAA

               
       2233 GAG
          1 GAG

       2236 TGGAAAAGGA


Statistics
Matches: 26,  Mismatches: 4, Indels: 1
        0.84            0.13        0.03

Matches are distributed among these distances:
  27    4  0.15
  28   22  0.85

ACGTcount: A:0.66, C:0.00, G:0.34, T:0.00


Consensus pattern (27 bp):   
GAGGAAGAAAGAAAAGAAAAAAGAAAA
Done.