Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01017786.1 Corchorus olitorius cultivar O-4 contig17819, 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: 1908
ACGTcount: A:0.35, C:0.14, G:0.14, T:0.38


Found at i:151 original size:70 final size:70

Alignment explanation


    Indices: 38--182  Score: 263
    Period size: 70  Copynumber: 2.1  Consensus size: 70

         28 TGCATGTTTG

                                       *                                     
         38 TGTGTAGAACGTTGTTTTGGAGAAAATGTTTATTTCGAATGTGTTATTTATGTAATCAATGCTCA
          1 TGTGTAGAACGTTGTTTTGGAGAAAATATTTATTTCGAATGTGTTATTTATGTAATCAATGCTCA

                 
        103 TATGT
         66 TATGT

                                                             *      *        
        108 TGTGTAGAACGTTGTTTTGGAGAAAATATTTATTTCGAATGTGTTATTTGTGTAATTAATGCTCA
          1 TGTGTAGAACGTTGTTTTGGAGAAAATATTTATTTCGAATGTGTTATTTATGTAATCAATGCTCA

                 
        173 TATGT
         66 TATGT

                 
        178 TGTGT
          1 TGTGT

        183 TTCAAAGTTA


Statistics
Matches: 72,  Mismatches: 3, Indels: 0
        0.96            0.04        0.00

Matches are distributed among these distances:
  70   72  1.00

ACGTcount: A:0.26, C:0.06, G:0.22, T:0.46


Consensus pattern (70 bp):   
TGTGTAGAACGTTGTTTTGGAGAAAATATTTATTTCGAATGTGTTATTTATGTAATCAATGCTCA
TATGT

Found at i:721 original size:38 final size:38

Alignment explanation


    Indices: 673--745  Score: 137
    Period size: 38  Copynumber: 1.9  Consensus size: 38

        663 ATATATAACC

                       *                          
        673 TTTTTCATAACTGTTATAGCTTTTTGAGTAATTAACTT
          1 TTTTTCATAACCGTTATAGCTTTTTGAGTAATTAACTT

                                               
        711 TTTTTCATAACCGTTATAGCTTTTTGAGTAATTAA
          1 TTTTTCATAACCGTTATAGCTTTTTGAGTAATTAA

        746 GTATTGTAAA


Statistics
Matches: 34,  Mismatches: 1, Indels: 0
        0.97            0.03        0.00

Matches are distributed among these distances:
  38   34  1.00

ACGTcount: A:0.27, C:0.11, G:0.11, T:0.51


Consensus pattern (38 bp):   
TTTTTCATAACCGTTATAGCTTTTTGAGTAATTAACTT

Found at i:1014 original size:13 final size:13

Alignment explanation


    Indices: 996--1020  Score: 50
    Period size: 13  Copynumber: 1.9  Consensus size: 13

        986 GTAAATTTGA

                         
        996 TAATTACTGTAAC
          1 TAATTACTGTAAC

                        
       1009 TAATTACTGTAA
          1 TAATTACTGTAA

       1021 ATTTGATAAC


Statistics
Matches: 12,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  13   12  1.00

ACGTcount: A:0.40, C:0.12, G:0.08, T:0.40


Consensus pattern (13 bp):   
TAATTACTGTAAC
Done.