Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01020091.1 Corchorus olitorius cultivar O-4 contig20124, 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: 3423
ACGTcount: A:0.34, C:0.14, G:0.21, T:0.31


Found at i:702 original size:20 final size:20

Alignment explanation


    Indices: 677--717  Score: 82
    Period size: 20  Copynumber: 2.0  Consensus size: 20

        667 CGTATCTCTT

                                
        677 TGTGGCAGAAGTCAGTAATG
          1 TGTGGCAGAAGTCAGTAATG

                                
        697 TGTGGCAGAAGTCAGTAATG
          1 TGTGGCAGAAGTCAGTAATG

             
        717 T
          1 T

        718 ATGGAAGAAA


Statistics
Matches: 21,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  20   21  1.00

ACGTcount: A:0.29, C:0.10, G:0.34, T:0.27


Consensus pattern (20 bp):   
TGTGGCAGAAGTCAGTAATG

Found at i:726 original size:20 final size:20

Alignment explanation


    Indices: 683--726  Score: 70
    Period size: 20  Copynumber: 2.2  Consensus size: 20

        673 TCTTTGTGGC

                           *   *
        683 AGAAGTCAGTAATGTGTGGC
          1 AGAAGTCAGTAATGTATGGA

                                
        703 AGAAGTCAGTAATGTATGGA
          1 AGAAGTCAGTAATGTATGGA

                
        723 AGAA
          1 AGAA

        727 AGATTGATAT


Statistics
Matches: 22,  Mismatches: 2, Indels: 0
        0.92            0.08        0.00

Matches are distributed among these distances:
  20   22  1.00

ACGTcount: A:0.39, C:0.07, G:0.32, T:0.23


Consensus pattern (20 bp):   
AGAAGTCAGTAATGTATGGA

Found at i:2877 original size:12 final size:12

Alignment explanation


    Indices: 2854--2887  Score: 50
    Period size: 12  Copynumber: 2.8  Consensus size: 12

       2844 CCAAACGCTA

                         
       2854 GGCCAGGCGCATG
          1 GGCCA-GCGCATG

                        
       2867 GGCCAGCGCATG
          1 GGCCAGCGCATG

             *       
       2879 GCCCAGCGC
          1 GGCCAGCGC

       2888 CTAGGCTAAG


Statistics
Matches: 20,  Mismatches: 1, Indels: 1
        0.91            0.05        0.05

Matches are distributed among these distances:
  12   15  0.75
  13    5  0.25

ACGTcount: A:0.15, C:0.38, G:0.41, T:0.06


Consensus pattern (12 bp):   
GGCCAGCGCATG

Found at i:2999 original size:24 final size:26

Alignment explanation


    Indices: 2958--3005  Score: 66
    Period size: 24  Copynumber: 1.9  Consensus size: 26

       2948 GCCCAATGTG

                                      
       2958 AAATAAAAGAAAGAAATAA-AAATAA
          1 AAATAAAAGAAAGAAATAAGAAATAA

                                     
       2983 AAAT-AAAGAAA-ATAATAAGAAAT
          1 AAATAAAAGAAAGA-AATAAGAAAT

       3006 TTTAGAATAA


Statistics
Matches: 21,  Mismatches: 0, Indels: 4
        0.84            0.00        0.16

Matches are distributed among these distances:
  23    1  0.05
  24   12  0.57
  25    8  0.38

ACGTcount: A:0.77, C:0.00, G:0.08, T:0.15


Consensus pattern (26 bp):   
AAATAAAAGAAAGAAATAAGAAATAA
Done.