Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01008180.1 Corchorus capsularis cultivar CVL-1 contig08201, 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: 4656
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.33


Found at i:1096 original size:206 final size:206

Alignment explanation


    Indices: 735--1124  Score: 726
    Period size: 206  Copynumber: 1.9  Consensus size: 206

        725 TTGGTGGGTT

                                                                             
        735 CCACTCTTAATAAACAAATCATTTTTTGTTGGATTATTTATCAAATGATTCTCATACTTTTATGT
          1 CCACTCTTAATAAACAAATCATTTTTTGTTGGATTATTTATCAAATGATTCTCATACTTTTATGT

                                                              **             
        800 TTTATGCTATTTAATCCTTTACAATTATGGGTTGGACGATTGAATATTTCGGCTTTAATTCTTTT
         66 TTTATGCTATTTAATCCTTTACAATTATGGGTTGGACGATTGAATATTTCAACTTTAATTCTTTT

                              *                                              
        865 ATTTCTTTTCTATTTGTCTGATCAAGGTAATTCAGGTGTCTATTTAAAGGTAATGGACAAATCAT
        131 ATTTCTTTTCTATTTGTCCGATCAAGGTAATTCAGGTGTCTATTTAAAGGTAATGGACAAATCAT

                       
        930 TTTAGTGGATC
        196 TTTAGTGGATC

                     *                                                       
        941 CCACTCTTAGTAAACAAATCATTTTTTGTTGGATTATTTATCAAATGATTCTCATACTTTTATGT
          1 CCACTCTTAATAAACAAATCATTTTTTGTTGGATTATTTATCAAATGATTCTCATACTTTTATGT

                                                         *                   
       1006 TTTATGCTATTTAATCCTTTACAATTATGGGTTGGACGATTGAATGTTTCAACTTTAATTCTTTT
         66 TTTATGCTATTTAATCCTTTACAATTATGGGTTGGACGATTGAATATTTCAACTTTAATTCTTTT

                *                                                 
       1071 ATTTTTTTTCTATTTGTCCGATCAAGGTAATTCAGGTGTCTATTTAAAGGTAAT
        131 ATTTCTTTTCTATTTGTCCGATCAAGGTAATTCAGGTGTCTATTTAAAGGTAAT

       1125 TTCATGGTCT


Statistics
Matches: 178,  Mismatches: 6, Indels: 0
        0.97            0.03        0.00

Matches are distributed among these distances:
 206  178  1.00

ACGTcount: A:0.27, C:0.13, G:0.14, T:0.46


Consensus pattern (206 bp):   
CCACTCTTAATAAACAAATCATTTTTTGTTGGATTATTTATCAAATGATTCTCATACTTTTATGT
TTTATGCTATTTAATCCTTTACAATTATGGGTTGGACGATTGAATATTTCAACTTTAATTCTTTT
ATTTCTTTTCTATTTGTCCGATCAAGGTAATTCAGGTGTCTATTTAAAGGTAATGGACAAATCAT
TTTAGTGGATC

Found at i:1797 original size:24 final size:23

Alignment explanation


    Indices: 1764--1825  Score: 106
    Period size: 24  Copynumber: 2.6  Consensus size: 23

       1754 TAATGTCCAT

                                   
       1764 TACAGCTACGCAAATACAAAAAC
          1 TACAGCTACGCAAATACAAAAAC

                                    
       1787 TAACAGCTACGCAAATACAAAAAC
          1 T-ACAGCTACGCAAATACAAAAAC

                           
       1811 TACAAGCTACGCAAA
          1 TAC-AGCTACGCAAA

       1826 ATCAACTATC


Statistics
Matches: 37,  Mismatches: 0, Indels: 3
        0.93            0.00        0.08

Matches are distributed among these distances:
  23    3  0.08
  24   34  0.92

ACGTcount: A:0.52, C:0.26, G:0.10, T:0.13


Consensus pattern (23 bp):   
TACAGCTACGCAAATACAAAAAC
Done.