Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01017182.1 Corchorus olitorius cultivar O-4 contig17215, 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: 14613
ACGTcount: A:0.30, C:0.17, G:0.21, T:0.32


Found at i:47 original size:30 final size:29

Alignment explanation


    Indices: 1--101  Score: 141
    Period size: 29  Copynumber: 3.5  Consensus size: 29

                    *         *     *     
          1 ATTTTGGTTA-TTTTGCATATCCGGGGGGC
          1 ATTTTGGTCATTTTTGCACATCC-AGGGGC

                                  *      
         30 ATTTTGGTCATTTTTGCACATCTAGGGGC
          1 ATTTTGGTCATTTTTGCACATCCAGGGGC

                 *                       
         59 ATTTTAGTCATTTTTGCACATCCAGGGGC
          1 ATTTTGGTCATTTTTGCACATCCAGGGGC

                          
         88 ATTTTGGTCATTTT
          1 ATTTTGGTCATTTT

        102 GGTTTTATTC


Statistics
Matches: 64,  Mismatches: 7, Indels: 2
        0.88            0.10        0.03

Matches are distributed among these distances:
  29   54  0.84
  30   10  0.16

ACGTcount: A:0.17, C:0.16, G:0.24, T:0.44


Consensus pattern (29 bp):   
ATTTTGGTCATTTTTGCACATCCAGGGGC

Found at i:1109 original size:17 final size:17

Alignment explanation


    Indices: 1087--1119  Score: 57
    Period size: 17  Copynumber: 1.9  Consensus size: 17

       1077 AAACTCAGAA

                             
       1087 AGCAGAATTCTAAATGC
          1 AGCAGAATTCTAAATGC

                  *         
       1104 AGCAGAGTTCTAAATG
          1 AGCAGAATTCTAAATG

       1120 GCAAGGCAAA


Statistics
Matches: 15,  Mismatches: 1, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
  17   15  1.00

ACGTcount: A:0.39, C:0.15, G:0.21, T:0.24


Consensus pattern (17 bp):   
AGCAGAATTCTAAATGC

Found at i:8414 original size:29 final size:29

Alignment explanation


    Indices: 8372--8427  Score: 94
    Period size: 29  Copynumber: 1.9  Consensus size: 29

       8362 TACAAGTTTA

                          *   *          
       8372 CAACACCACAATTATAAGTTTTCAACAAT
          1 CAACACCACAATTACAAGCTTTCAACAAT

                                       
       8401 CAACACCACAATTACAAGCTTTCAACA
          1 CAACACCACAATTACAAGCTTTCAACA

       8428 CCATACAAGG


Statistics
Matches: 25,  Mismatches: 2, Indels: 0
        0.93            0.07        0.00

Matches are distributed among these distances:
  29   25  1.00

ACGTcount: A:0.45, C:0.29, G:0.04, T:0.23


Consensus pattern (29 bp):   
CAACACCACAATTACAAGCTTTCAACAAT
Done.