Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01012712.1 Corchorus olitorius cultivar O-4 contig12745, 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: 10006
ACGTcount: A:0.30, C:0.15, G:0.17, T:0.39


Found at i:29 original size:22 final size:22

Alignment explanation


    Indices: 1--147  Score: 123
    Period size: 22  Copynumber: 6.3  Consensus size: 22

                       **         
          1 AGAGCATTATTCACCACTTTGC
          1 AGAGCATTATTTTCCACTTTGC

                                  
         23 AGAGCATTATTTTCCACTTTGC
          1 AGAGCATTATTTTCCACTTTGC

                                * 
         45 AGAGCATTATTTTCCACTTTAC
          1 AGAGCATTATTTTCCACTTTGC

                                     *  
         67 AGAGTGCATTATTTTCTTCAACTTCAGC
          1 AGA--GCATTATTTTC--C-ACTT-TGC

            ***          ***         
         95 TTTGCATTATTGGAAACATCTTTGC
          1 AGAGCATTATT--TTCCA-CTTTGC

                                  
        120 AGAGCATTATTTTCCACTTTGC
          1 AGAGCATTATTTTCCACTTTGC

                  
        142 AGAGCA
          1 AGAGCA

        148 CTTCTTGTTG


Statistics
Matches: 98,  Mismatches: 18, Indels: 18
        0.73            0.13        0.13

Matches are distributed among these distances:
  22   56  0.57
  23    2  0.02
  24   11  0.11
  25   11  0.11
  26   13  0.13
  27    4  0.04
  28    1  0.01

ACGTcount: A:0.26, C:0.22, G:0.14, T:0.38


Consensus pattern (22 bp):   
AGAGCATTATTTTCCACTTTGC

Found at i:5521 original size:34 final size:34

Alignment explanation


    Indices: 5483--5551  Score: 138
    Period size: 34  Copynumber: 2.0  Consensus size: 34

       5473 GATGGAACTG

                                              
       5483 AAAAATGGAAAGGAGAAATCGAAGCTCTTCGGTT
          1 AAAAATGGAAAGGAGAAATCGAAGCTCTTCGGTT

                                              
       5517 AAAAATGGAAAGGAGAAATCGAAGCTCTTCGGTT
          1 AAAAATGGAAAGGAGAAATCGAAGCTCTTCGGTT

             
       5551 A
          1 A

       5552 GGTGCGATTT


Statistics
Matches: 35,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  34   35  1.00

ACGTcount: A:0.42, C:0.12, G:0.26, T:0.20


Consensus pattern (34 bp):   
AAAAATGGAAAGGAGAAATCGAAGCTCTTCGGTT
Done.