Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01013506.1 Corchorus olitorius cultivar O-4 contig13539, 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: 5093
ACGTcount: A:0.35, C:0.19, G:0.16, T:0.30


Found at i:2174 original size:29 final size:28

Alignment explanation


    Indices: 2118--2174  Score: 69
    Period size: 28  Copynumber: 2.0  Consensus size: 28

       2108 TAAAGGAAAT

                    **            *     
       2118 TTTTTTTTTGAAAACGCAAAAATAAGAA
          1 TTTTTTTTCAAAAACGCAAAAAGAAGAA

                                    *    
       2146 TTTTTTTTCAAAAACGCAAAGAAGCAGAA
          1 TTTTTTTTCAAAAACGCAAA-AAGAAGAA

       2175 ATTAAAAACG


Statistics
Matches: 24,  Mismatches: 4, Indels: 1
        0.83            0.14        0.03

Matches are distributed among these distances:
  28   18  0.75
  29    6  0.25

ACGTcount: A:0.46, C:0.11, G:0.12, T:0.32


Consensus pattern (28 bp):   
TTTTTTTTCAAAAACGCAAAAAGAAGAA

Found at i:3273 original size:18 final size:17

Alignment explanation


    Indices: 3250--3286  Score: 56
    Period size: 18  Copynumber: 2.1  Consensus size: 17

       3240 CTAACCCTAA

                              
       3250 AACTAGAAGAAAAACAAG
          1 AACTAGAAGAAAAA-AAG

                      *      
       3268 AACTAGAAGAGAAAAAG
          1 AACTAGAAGAAAAAAAG

              
       3285 AA
          1 AA

       3287 GAGCAAATTA


Statistics
Matches: 18,  Mismatches: 1, Indels: 1
        0.90            0.05        0.05

Matches are distributed among these distances:
  17    5  0.28
  18   13  0.72

ACGTcount: A:0.68, C:0.08, G:0.19, T:0.05


Consensus pattern (17 bp):   
AACTAGAAGAAAAAAAG
Done.