Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01018009.1 Corchorus olitorius cultivar O-4 contig18042, 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: 2102
ACGTcount: A:0.30, C:0.15, G:0.20, T:0.35


Found at i:680 original size:6 final size:6

Alignment explanation


    Indices: 669--700  Score: 55
    Period size: 6  Copynumber: 5.3  Consensus size: 6

        659 CACTCTTTGA

                                          *      
        669 AAAAAT AAAAAT AAAAAT AAAAAT AATAAT AA
          1 AAAAAT AAAAAT AAAAAT AAAAAT AAAAAT AA

        701 GGTTAGTAAC


Statistics
Matches: 25,  Mismatches: 1, Indels: 0
        0.96            0.04        0.00

Matches are distributed among these distances:
   6   25  1.00

ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19


Consensus pattern (6 bp):   
AAAAAT

Found at i:1832 original size:76 final size:76

Alignment explanation


    Indices: 1739--1890  Score: 175
    Period size: 76  Copynumber: 2.0  Consensus size: 76

       1729 TGATGAGCTA

                        *      *    *       *                                
       1739 TGACACAGCCCATCTGGGTGATCAGGCGAAA-GACATGGGT-CTTC-AGACAAACCATGTGGGCA
          1 TGACACAGCCCACCTGGGTCATCAAGC-AAACCACATGGGTGC-TCAAGAC-AACCATGTGGGCA

                          
       1801 CCCAGCTGGAGTCG
         63 CCCAGCTGGAGTCG

                  *             *                          *             *   
       1815 TGACACTGCCCACCTGGGTCCTCAAGCAAACCACATGGGTGCTCAAGGCAACCATGTGGGCGCCC
          1 TGACACAGCCCACCTGGGTCATCAAGCAAACCACATGGGTGCTCAAGACAACCATGTGGGCACCC

              *        
       1880 AGGTGGAGTCG
         66 AGCTGGAGTCG

       1891 GGGTCCTTGC


Statistics
Matches: 64,  Mismatches: 9, Indels: 6
        0.81            0.11        0.08

Matches are distributed among these distances:
  75    3  0.05
  76   57  0.89
  77    4  0.06

ACGTcount: A:0.24, C:0.29, G:0.30, T:0.16


Consensus pattern (76 bp):   
TGACACAGCCCACCTGGGTCATCAAGCAAACCACATGGGTGCTCAAGACAACCATGTGGGCACCC
AGCTGGAGTCG
Done.