Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01013315.1 Corchorus olitorius cultivar O-4 contig13348, 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: 6570
ACGTcount: A:0.31, C:0.18, G:0.19, T:0.31


Found at i:3974 original size:10 final size:10

Alignment explanation


    Indices: 3959--3988  Score: 51
    Period size: 10  Copynumber: 3.0  Consensus size: 10

       3949 ATCCGAGCCT

                      
       3959 CATGCCCGGC
          1 CATGCCCGGC

                   *  
       3969 CATGCCCAGC
          1 CATGCCCGGC

                      
       3979 CATGCCCGGC
          1 CATGCCCGGC

       3989 ACCACAAGCC


Statistics
Matches: 18,  Mismatches: 2, Indels: 0
        0.90            0.10        0.00

Matches are distributed among these distances:
  10   18  1.00

ACGTcount: A:0.13, C:0.50, G:0.27, T:0.10


Consensus pattern (10 bp):   
CATGCCCGGC

Found at i:4188 original size:22 final size:21

Alignment explanation


    Indices: 4163--4208  Score: 56
    Period size: 21  Copynumber: 2.1  Consensus size: 21

       4153 CCAAACCATT

                                  
       4163 ACCGCCCATTCCTCGTGCCACC
          1 ACCGCCCA-TCCTCGTGCCACC

                *    *         * 
       4185 ACCGGCCATGCTCGTGCCATC
          1 ACCGCCCATCCTCGTGCCACC

               
       4206 ACC
          1 ACC

       4209 ATTCCATGCC


Statistics
Matches: 21,  Mismatches: 3, Indels: 1
        0.84            0.12        0.04

Matches are distributed among these distances:
  21   14  0.67
  22    7  0.33

ACGTcount: A:0.15, C:0.50, G:0.17, T:0.17


Consensus pattern (21 bp):   
ACCGCCCATCCTCGTGCCACC

Found at i:5125 original size:18 final size:18

Alignment explanation


    Indices: 5102--5138  Score: 56
    Period size: 18  Copynumber: 2.1  Consensus size: 18

       5092 AAAGGGTAGT

                     *        
       5102 TAAAAAAAATTGTTTTCA
          1 TAAAAAAAAGTGTTTTCA

                  *           
       5120 TAAAAAGAAGTGTTTTCA
          1 TAAAAAAAAGTGTTTTCA

             
       5138 T
          1 T

       5139 GCAAGAGGAG


Statistics
Matches: 17,  Mismatches: 2, Indels: 0
        0.89            0.11        0.00

Matches are distributed among these distances:
  18   17  1.00

ACGTcount: A:0.46, C:0.05, G:0.11, T:0.38


Consensus pattern (18 bp):   
TAAAAAAAAGTGTTTTCA
Done.