Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01001746.1 Corchorus olitorius cultivar O-4 contig01746, 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, 687

Length: 1146
ACGTcount: A:0.27, C:0.29, G:0.21, T:0.22


Found at i:800 original size:54 final size:54

Alignment explanation


    Indices: 736--858  Score: 169
    Period size: 54  Copynumber: 2.3  Consensus size: 54

        726 CACCTGCCCG

                                        *         *                
        736 GCCACA-GCCCGGCCACCCGAGCC-TCATGCCCAGCCATCAGCGCTACCATCCGA
          1 GCCACATGCCCGGCCACCCGAGCCATC-CGCCCAGCCACCAGCGCTACCATCCGA

                                           **                    *
        789 GCCACATGCCCGGCCACCCGAGCCATCCGCCTGGCCACCAGCGCTACCATCCGC
          1 GCCACATGCCCGGCCACCCGAGCCATCCGCCCAGCCACCAGCGCTACCATCCGA

                   *        
        843 GCCACATTCCCGGCCA
          1 GCCACATGCCCGGCCA

        859 TCCGCGCTAT


Statistics
Matches: 62,  Mismatches: 6, Indels: 3
        0.87            0.08        0.04

Matches are distributed among these distances:
  53    6  0.10
  54   54  0.87
  55    2  0.03

ACGTcount: A:0.19, C:0.50, G:0.21, T:0.10


Consensus pattern (54 bp):   
GCCACATGCCCGGCCACCCGAGCCATCCGCCCAGCCACCAGCGCTACCATCCGA

Found at i:1077 original size:22 final size:21

Alignment explanation


    Indices: 1046--1097  Score: 59
    Period size: 21  Copynumber: 2.4  Consensus size: 21

       1036 CCACTACCAA

                 *        **      
       1046 GCCACAACCGGTCATTCACCGT
          1 GCCACCACCGGTCAAGC-CCGT

                        *        
       1068 GCCACCACCGGTTAAGCCCGT
          1 GCCACCACCGGTCAAGCCCGT

                     
       1089 GCCACCACC
          1 GCCACCACC

       1098 ACCGGCCATG


Statistics
Matches: 26,  Mismatches: 4, Indels: 1
        0.84            0.13        0.03

Matches are distributed among these distances:
  21   13  0.50
  22   13  0.50

ACGTcount: A:0.21, C:0.46, G:0.19, T:0.13


Consensus pattern (21 bp):   
GCCACCACCGGTCAAGCCCGT

Found at i:1101 original size:24 final size:24

Alignment explanation


    Indices: 1069--1122  Score: 72
    Period size: 24  Copynumber: 2.2  Consensus size: 24

       1059 ATTCACCGTG

                      **            
       1069 CCACCACCGGTTAAGCCCGTGCCA
          1 CCACCACCGGCCAAGCCCGTGCCA

                         *          
       1093 CCACCACCGGCCATGCCCGTGCCA
          1 CCACCACCGGCCAAGCCCGTGCCA

            *     
       1117 TCACCA
          1 CCACCA

       1123 TTCCATGCCG


Statistics
Matches: 26,  Mismatches: 4, Indels: 0
        0.87            0.13        0.00

Matches are distributed among these distances:
  24   26  1.00

ACGTcount: A:0.20, C:0.50, G:0.19, T:0.11


Consensus pattern (24 bp):   
CCACCACCGGCCAAGCCCGTGCCA
Done.