Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01017005.1 Corchorus olitorius cultivar O-4 contig17038, 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: 3809
ACGTcount: A:0.32, C:0.21, G:0.20, T:0.28


Found at i:2077 original size:54 final size:54

Alignment explanation


    Indices: 2019--2137  Score: 186
    Period size: 54  Copynumber: 2.2  Consensus size: 54

       2009 CGGCCATAGC

                                         *                         
       2019 TCGGCCATCCGAGCCATCTGCCTGGCCACGCCCGGACTC-CTCCGCGCACCACAA
          1 TCGGCCATCCGAGCCATCTGCCTGGCCACACCCGGAC-CACTCCGCGCACCACAA

                   *                               *              
       2073 TCGGCCACCCGAGCCATCTGCCTGGCCACACCCGGACCAGTCCGCGCACCACAA
          1 TCGGCCATCCGAGCCATCTGCCTGGCCACACCCGGACCACTCCGCGCACCACAA

            *          
       2127 CCGGCCATCCG
          1 TCGGCCATCCG

       2138 CGCCGCCTGC


Statistics
Matches: 59,  Mismatches: 5, Indels: 2
        0.89            0.08        0.03

Matches are distributed among these distances:
  53    1  0.02
  54   58  0.98

ACGTcount: A:0.18, C:0.49, G:0.23, T:0.11


Consensus pattern (54 bp):   
TCGGCCATCCGAGCCATCTGCCTGGCCACACCCGGACCACTCCGCGCACCACAA

Found at i:2139 original size:21 final size:23

Alignment explanation


    Indices: 2098--2140  Score: 63
    Period size: 23  Copynumber: 2.0  Consensus size: 23

       2088 ATCTGCCTGG

                 *                 
       2098 CCACACCCGGACCAGTCCGCGCA
          1 CCACAACCGGACCAGTCCGCGCA

                                  
       2121 CCACAACCGG-CCA-TCCGCGC
          1 CCACAACCGGACCAGTCCGCGC

       2141 CGCCTGCCCA


Statistics
Matches: 19,  Mismatches: 1, Indels: 2
        0.86            0.05        0.09

Matches are distributed among these distances:
  21    7  0.37
  22    3  0.16
  23    9  0.47

ACGTcount: A:0.21, C:0.53, G:0.21, T:0.05


Consensus pattern (23 bp):   
CCACAACCGGACCAGTCCGCGCA

Done.