Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01006864.1 Corchorus capsularis cultivar CVL-1 contig06885, 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: 19583
ACGTcount: A:0.31, C:0.19, G:0.18, T:0.32


Found at i:5245 original size:64 final size:64

Alignment explanation


    Indices: 5121--5245  Score: 148
    Period size: 64  Copynumber: 2.0  Consensus size: 64

       5111 CTCGTCCGGT

                                       *      *                             
       5121 GCCGCCCCAGAAGGGAGGCAAGCACGGTGCAAACTGCCCTAATAGGACGGCATTCCATGGTGAA
          1 GCCGCCCCAGAAGGGAGGCAAGCACGGAGCAAACCGCCCTAATAGGACGGCATTCCATGGTGAA

                      *    *    *                           *               
       5185 GCCGCCCCAGGAGGGCGGCATGCGACGGAG-AAACCGCCC-AACTAGGGCGGC-TTCACATGGT
          1 GCCGCCCCAGAAGGGAGGCAAGC-ACGGAGCAAACCGCCCTAA-TAGGACGGCATTC-CATGGT

       5246 CAGGCCGCAC


Statistics
Matches: 52,  Mismatches: 6, Indels: 6
        0.81            0.09        0.09

Matches are distributed among these distances:
  63    5  0.10
  64   42  0.81
  65    5  0.10

ACGTcount: A:0.25, C:0.30, G:0.34, T:0.11


Consensus pattern (64 bp):   
GCCGCCCCAGAAGGGAGGCAAGCACGGAGCAAACCGCCCTAATAGGACGGCATTCCATGGTGAA

Found at i:6049 original size:11 final size:11

Alignment explanation


    Indices: 6033--6076  Score: 52
    Period size: 11  Copynumber: 3.7  Consensus size: 11

       6023 AGCGGTATTA

                       
       6033 TTTTCAACTTG
          1 TTTTCAACTTG

                         *
       6044 TTTTCAACGTATTA
          1 TTTTCAAC---TTG

                       
       6058 TTTTCAACTTG
          1 TTTTCAACTTG

                    
       6069 TTTTCAAC
          1 TTTTCAAC

       6077 GTGGGTTTTA


Statistics
Matches: 28,  Mismatches: 2, Indels: 6
        0.78            0.06        0.17

Matches are distributed among these distances:
  11   18  0.64
  14   10  0.36

ACGTcount: A:0.23, C:0.18, G:0.07, T:0.52


Consensus pattern (11 bp):   
TTTTCAACTTG

Found at i:6061 original size:25 final size:25

Alignment explanation


    Indices: 6027--6078  Score: 104
    Period size: 25  Copynumber: 2.1  Consensus size: 25

       6017 GCCGGAAGCG

                                     
       6027 GTATTATTTTCAACTTGTTTTCAAC
          1 GTATTATTTTCAACTTGTTTTCAAC

                                     
       6052 GTATTATTTTCAACTTGTTTTCAAC
          1 GTATTATTTTCAACTTGTTTTCAAC

              
       6077 GT
          1 GT

       6079 GGGTTTTATT


Statistics
Matches: 27,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  25   27  1.00

ACGTcount: A:0.23, C:0.15, G:0.10, T:0.52


Consensus pattern (25 bp):   
GTATTATTTTCAACTTGTTTTCAAC
Done.