Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01013787.1 Corchorus olitorius cultivar O-4 contig13820, 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: 4056
ACGTcount: A:0.32, C:0.21, G:0.16, T:0.31


Found at i:2113 original size:33 final size:33

Alignment explanation


    Indices: 1965--2149  Score: 124
    Period size: 33  Copynumber: 5.6  Consensus size: 33

       1955 ATTTATTGGT

                    **         * *        * *
       1965 GCCGCCCAAGGAGGGCGGCGTAACCATGGCTAT
          1 GCCGCCCACTGAGGGCGGCATGACCATGGCCAC

                    **    *                   
       1998 GCCGCCCAAGGAGGACGGCATGGA-CATGGCCAC
          1 GCCGCCCACTGAGGGCGGCAT-GACCATGGCCAC

                            *     *       ** *
       2031 GCCGCCCACTGAGGGCCGCAT-CCCAATGGTTAG
          1 GCCGCCCACTGAGGGCGGCATGACC-ATGGCCAC

             *      *   *                     
       2064 GGCGCCCTCCT-TGGGCGGCATGACCATGGCCAC
          1 GCCGCCC-ACTGAGGGCGGCATGACCATGGCCAC

                                 **         *
       2097 GCCGCCCACTGAGGGCGGCATCCCCATGGCCAT
          1 GCCGCCCACTGAGGGCGGCATGACCATGGCCAC

                   * *          
       2130 GCCGCCCTCCGAGGGCGGCA
          1 GCCGCCCACTGAGGGCGGCA

       2150 CCGACCATTT


Statistics
Matches: 117,  Mismatches: 29, Indels: 12
        0.74            0.18        0.08

Matches are distributed among these distances:
  32    3  0.03
  33  109  0.93
  34    5  0.04

ACGTcount: A:0.17, C:0.37, G:0.34, T:0.11


Consensus pattern (33 bp):   
GCCGCCCACTGAGGGCGGCATGACCATGGCCAC

Found at i:2136 original size:66 final size:66

Alignment explanation


    Indices: 2008--2149  Score: 187
    Period size: 66  Copynumber: 2.2  Consensus size: 66

       1998 GCCGCCCAAG

                *                                               **   *       
       2008 GAGGACGGCATGGACATGGCCACGCCGCCCACTGAGGGCCGCATCCCAATGGTTAGGGCGCCCTC
          1 GAGGGCGGCATGGACATGGCCACGCCGCCCACTGAGGGCCGCATCCCAATGGCCAGGCCGCCCTC

             
       2073 C
         66 C

            **                                      *       *       *        
       2074 TTGGGCGGCAT-GACCATGGCCACGCCGCCCACTGAGGGCGGCATCCCCATGGCCATGCCGCCCT
          1 GAGGGCGGCATGGA-CATGGCCACGCCGCCCACTGAGGGCCGCATCCCAATGGCCAGGCCGCCCT

              
       2138 CC
         65 CC

                      
       2140 GAGGGCGGCA
          1 GAGGGCGGCA

       2150 CCGACCATTT


Statistics
Matches: 64,  Mismatches: 11, Indels: 2
        0.83            0.14        0.03

Matches are distributed among these distances:
  65    2  0.03
  66   62  0.97

ACGTcount: A:0.16, C:0.38, G:0.34, T:0.12


Consensus pattern (66 bp):   
GAGGGCGGCATGGACATGGCCACGCCGCCCACTGAGGGCCGCATCCCAATGGCCAGGCCGCCCTC
C

Found at i:3948 original size:29 final size:30

Alignment explanation


    Indices: 3894--3967  Score: 96
    Period size: 29  Copynumber: 2.5  Consensus size: 30

       3884 TACCCAGAAA

                *               *          
       3894 AATCTCTTATGTTTTACTTTTGGGACAAAAT
          1 AATCCCTTATGTTTTA-TTTCGGGACAAAAT

                                        * 
       3925 AATCCCTTATGTTTT-TTTCGGGACAAATT
          1 AATCCCTTATGTTTTATTTCGGGACAAAAT

                     *    
       3954 AATCCCTTACGTTT
          1 AATCCCTTATGTTT

       3968 CAAAAATGAG


Statistics
Matches: 39,  Mismatches: 4, Indels: 2
        0.87            0.09        0.04

Matches are distributed among these distances:
  29   25  0.64
  31   14  0.36

ACGTcount: A:0.26, C:0.18, G:0.12, T:0.45


Consensus pattern (30 bp):   
AATCCCTTATGTTTTATTTCGGGACAAAAT
Done.