Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01010423.1 Corchorus olitorius cultivar O-4 contig10455, 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: 6004
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36


Found at i:63 original size:30 final size:30

Alignment explanation


    Indices: 29--188  Score: 151
    Period size: 27  Copynumber: 5.6  Consensus size: 30

         19 GGTCACTTAA

                      *                   
         29 GGGCATTTTGATCATTTCTGCACATTTCAG
          1 GGGCATTTTGGTCATTTCTGCACATTTCAG

                                   *       
         59 GGGCATTTTGGTCATTTCT--ACGTATTCAG
          1 GGGCATTTTGGTCATTTCTGCACAT-TTCAG

            *  *         *         *       
         88 TGGTATTTTGGTCGTTTCTGCATGA-TTCAG
          1 GGGCATTTTGGTCATTTCTGCA-CATTTCAG

                                         *
        118 GGGCATTTTGGTCA-TT-TGCACA-TTCAA
          1 GGGCATTTTGGTCATTTCTGCACATTTCAG

                                           
        145 GGGCATTTTGGTCA-TT-TG--CATGTTCAG
          1 GGGCATTTTGGTCATTTCTGCACAT-TTCAG

                      *      
        172 GGGCATTTTGATCATTT
          1 GGGCATTTTGGTCATTT

        189 TAAGTTCACT


Statistics
Matches: 109,  Mismatches: 14, Indels: 16
        0.78            0.10        0.12

Matches are distributed among these distances:
  25    2  0.02
  27   40  0.37
  28    9  0.08
  29   23  0.21
  30   34  0.31
  31    1  0.01

ACGTcount: A:0.17, C:0.16, G:0.24, T:0.42


Consensus pattern (30 bp):   
GGGCATTTTGGTCATTTCTGCACATTTCAG

Found at i:5464 original size:29 final size:29

Alignment explanation


    Indices: 5422--5485  Score: 101
    Period size: 29  Copynumber: 2.2  Consensus size: 29

       5412 TAATCATTAA

                  *          * *         
       5422 AATTCCGTCTACCAATATATGTGCTACAT
          1 AATTCCATCTACCAATAAACGTGCTACAT

                                         
       5451 AATTCCATCTACCAATAAACGTGCTACAT
          1 AATTCCATCTACCAATAAACGTGCTACAT

                  
       5480 AATTCC
          1 AATTCC

       5486 TTATAAATCT


Statistics
Matches: 32,  Mismatches: 3, Indels: 0
        0.91            0.09        0.00

Matches are distributed among these distances:
  29   32  1.00

ACGTcount: A:0.34, C:0.27, G:0.08, T:0.31


Consensus pattern (29 bp):   
AATTCCATCTACCAATAAACGTGCTACAT
Done.