Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01014696.1 Corchorus capsularis cultivar CVL-1 contig14717, 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: 16040
ACGTcount: A:0.31, C:0.19, G:0.18, T:0.32


Found at i:141 original size:30 final size:30

Alignment explanation


    Indices: 105--167  Score: 92
    Period size: 30  Copynumber: 2.1  Consensus size: 30

         95 TCTTCAAGGG

                       *                   
        105 GGAGGGAATGATGCACCCAAGG-CTTATCAT
          1 GGAGGGAATGAAGC-CCCAAGGACTTATCAT

                          *               
        135 GGAGGGAATGAAGCGCCAAGGACTTATCAT
          1 GGAGGGAATGAAGCCCCAAGGACTTATCAT

               
        165 GGA
          1 GGA

        168 CTTGAAGATG


Statistics
Matches: 30,  Mismatches: 2, Indels: 2
        0.88            0.06        0.06

Matches are distributed among these distances:
  29    6  0.20
  30   24  0.80

ACGTcount: A:0.32, C:0.17, G:0.33, T:0.17


Consensus pattern (30 bp):   
GGAGGGAATGAAGCCCCAAGGACTTATCAT

Found at i:2032 original size:30 final size:30

Alignment explanation


    Indices: 1996--2058  Score: 101
    Period size: 30  Copynumber: 2.1  Consensus size: 30

       1986 TCTTCAAGGG

                       *                   
       1996 GGAGGGAATGATGCGCCCAAGG-CTTATCAT
          1 GGAGGGAATGAAGCG-CCAAGGACTTATCAT

                                          
       2026 GGAGGGAATGAAGCGCCAAGGACTTATCAT
          1 GGAGGGAATGAAGCGCCAAGGACTTATCAT

               
       2056 GGA
          1 GGA

       2059 CTTGAAGATG


Statistics
Matches: 31,  Mismatches: 1, Indels: 2
        0.91            0.03        0.06

Matches are distributed among these distances:
  29    6  0.19
  30   25  0.81

ACGTcount: A:0.30, C:0.17, G:0.35, T:0.17


Consensus pattern (30 bp):   
GGAGGGAATGAAGCGCCAAGGACTTATCAT

Found at i:3914 original size:30 final size:30

Alignment explanation


    Indices: 3878--3940  Score: 101
    Period size: 30  Copynumber: 2.1  Consensus size: 30

       3868 TCTTCAAGGG

                       *                   
       3878 GGAGGGAATGATGCGCCCAAGG-CTTATCAT
          1 GGAGGGAATGAAGCG-CCAAGGACTTATCAT

                                          
       3908 GGAGGGAATGAAGCGCCAAGGACTTATCAT
          1 GGAGGGAATGAAGCGCCAAGGACTTATCAT

               
       3938 GGA
          1 GGA

       3941 CTTGAAGATG


Statistics
Matches: 31,  Mismatches: 1, Indels: 2
        0.91            0.03        0.06

Matches are distributed among these distances:
  29    6  0.19
  30   25  0.81

ACGTcount: A:0.30, C:0.17, G:0.35, T:0.17


Consensus pattern (30 bp):   
GGAGGGAATGAAGCGCCAAGGACTTATCAT
Done.