Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01023624.1 Corchorus olitorius cultivar O-4 contig23657, 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: 20431
ACGTcount: A:0.33, C:0.18, G:0.19, T:0.30


Found at i:3153 original size:17 final size:17

Alignment explanation


    Indices: 3131--3166  Score: 54
    Period size: 17  Copynumber: 2.1  Consensus size: 17

       3121 ATTCATATAA

                      *      
       3131 AAATTGTCCATATAATG
          1 AAATTGTCCACATAATG

                   *         
       3148 AAATTGTTCACATAATG
          1 AAATTGTCCACATAATG

              
       3165 AA
          1 AA

       3167 GTTTAGCATA


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

Matches are distributed among these distances:
  17   17  1.00

ACGTcount: A:0.44, C:0.11, G:0.11, T:0.33


Consensus pattern (17 bp):   
AAATTGTCCACATAATG

Found at i:5065 original size:21 final size:22

Alignment explanation


    Indices: 5036--5077  Score: 59
    Period size: 21  Copynumber: 2.0  Consensus size: 22

       5026 GTTTATAATA

                *                 
       5036 TTCTTGGGTCA-TCGGGTTACC
          1 TTCTCGGGTCATTCGGGTTACC

                     *           
       5057 TTCTCGGGTTATTCGGGTTAC
          1 TTCTCGGGTCATTCGGGTTAC

       5078 GAGTTTGTCG


Statistics
Matches: 18,  Mismatches: 2, Indels: 1
        0.86            0.10        0.05

Matches are distributed among these distances:
  21    9  0.50
  22    9  0.50

ACGTcount: A:0.10, C:0.21, G:0.29, T:0.40


Consensus pattern (22 bp):   
TTCTCGGGTCATTCGGGTTACC

Found at i:19511 original size:28 final size:26

Alignment explanation


    Indices: 19470--19540  Score: 90
    Period size: 28  Copynumber: 2.7  Consensus size: 26

      19460 AAAAATCCAG

                                      * 
      19470 GGGCATTTTGGTCATTTTT-CACCATCA
          1 GGGCATTTTGGTCATTTTTACA-C-TAA

                    *                  
      19497 GTGGCATTATGGTCATTTTTACACTAA
          1 G-GGCATTTTGGTCATTTTTACACTAA

                             
      19524 GGGCATTTTGGTCATTT
          1 GGGCATTTTGGTCATTT

      19541 GAATATTCAG


Statistics
Matches: 39,  Mismatches: 3, Indels: 5
        0.83            0.06        0.11

Matches are distributed among these distances:
  26   15  0.38
  27    4  0.10
  28   18  0.46
  29    2  0.05

ACGTcount: A:0.20, C:0.17, G:0.21, T:0.42


Consensus pattern (26 bp):   
GGGCATTTTGGTCATTTTTACACTAA

Found at i:19535 original size:26 final size:27

Alignment explanation


    Indices: 19470--19540  Score: 92
    Period size: 26  Copynumber: 2.6  Consensus size: 27

      19460 AAAAATCCAG

                                     * 
      19470 GGGCATTTTGGTCATTTTTCACCATCA
          1 GGGCATTTTGGTCATTTTTCACCATAA

                    *                    
      19497 GTGGCATTATGGTCATTTTT-A-CACTAA
          1 G-GGCATTTTGGTCATTTTTCACCA-TAA

                             
      19524 GGGCATTTTGGTCATTT
          1 GGGCATTTTGGTCATTT

      19541 GAATATTCAG


Statistics
Matches: 39,  Mismatches: 3, Indels: 5
        0.83            0.06        0.11

Matches are distributed among these distances:
  26   17  0.44
  27    5  0.13
  28   17  0.44

ACGTcount: A:0.20, C:0.17, G:0.21, T:0.42


Consensus pattern (27 bp):   
GGGCATTTTGGTCATTTTTCACCATAA
Done.