Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01024120.1 Corchorus olitorius cultivar O-4 contig24153, 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: 11083
ACGTcount: A:0.33, C:0.18, G:0.16, T:0.33


Found at i:3198 original size:33 final size:32

Alignment explanation


    Indices: 3155--3242  Score: 115
    Period size: 31  Copynumber: 2.8  Consensus size: 32

       3145 TAGGTGTGGA

                 *                *  *       
       3155 GGCGTTCCCAGGGGGCGCCACAGCATGGTGGGT
          1 GGCGTCCCCA-GGGGCGCCACACCACGGTGGGT

                             *              
       3188 GGCGTCCCCAGGGG-GCAACACCACGGTGGGT
          1 GGCGTCCCCAGGGGCGCCACACCACGGTGGGT

              *                     
       3219 GGGGTCCCCAGGGGCGCCACACCA
          1 GGCGTCCCCAGGGGCGCCACACCA

       3243 TCGCCTCCAC


Statistics
Matches: 48,  Mismatches: 6, Indels: 3
        0.84            0.11        0.05

Matches are distributed among these distances:
  31   27  0.56
  32   12  0.25
  33    9  0.19

ACGTcount: A:0.15, C:0.33, G:0.42, T:0.10


Consensus pattern (32 bp):   
GGCGTCCCCAGGGGCGCCACACCACGGTGGGT

Found at i:5164 original size:57 final size:56

Alignment explanation


    Indices: 5076--5187  Score: 206
    Period size: 57  Copynumber: 2.0  Consensus size: 56

       5066 TATCCGTTTC

                                                           *         
       5076 CTTTCACACAATAAATGTTATAATAAATCCTATCCCCCCTATCTCTATTTAATTATT
          1 CTTTCACACAATAAATGTTATAATAAATCCTAT-CCCCCTATCTCTACTTAATTATT

                                                                   
       5133 CTTTCACACAATAAATGTTATAATAAATCCTATCCCCCTATCTCTACTTAATTAT
          1 CTTTCACACAATAAATGTTATAATAAATCCTATCCCCCTATCTCTACTTAATTAT

       5188 CCTACAAAAT


Statistics
Matches: 54,  Mismatches: 1, Indels: 1
        0.96            0.02        0.02

Matches are distributed among these distances:
  56   21  0.39
  57   33  0.61

ACGTcount: A:0.34, C:0.25, G:0.02, T:0.39


Consensus pattern (56 bp):   
CTTTCACACAATAAATGTTATAATAAATCCTATCCCCCTATCTCTACTTAATTATT

Found at i:6929 original size:50 final size:50

Alignment explanation


    Indices: 6854--6957  Score: 163
    Period size: 50  Copynumber: 2.1  Consensus size: 50

       6844 TAGCCTATGT

                           *                               *  
       6854 GTTTTCCAAACGCAAGCACAAGCTCGTTTACTAAACGCAAACACAGGTTC
          1 GTTTTCCAAACGCAAACACAAGCTCGTTTACTAAACGCAAACACAGGCTC

                                *        *          *         
       6904 GTTTTCCAAACGCAAACACAGGCTCGTTTGCTAAACGCAAGCACAGGCTC
          1 GTTTTCCAAACGCAAACACAAGCTCGTTTACTAAACGCAAACACAGGCTC

                
       6954 GTTT
          1 GTTT

       6958 GCTCAGCGCA


Statistics
Matches: 49,  Mismatches: 5, Indels: 0
        0.91            0.09        0.00

Matches are distributed among these distances:
  50   49  1.00

ACGTcount: A:0.31, C:0.28, G:0.18, T:0.23


Consensus pattern (50 bp):   
GTTTTCCAAACGCAAACACAAGCTCGTTTACTAAACGCAAACACAGGCTC

Found at i:6967 original size:25 final size:25

Alignment explanation


    Indices: 6861--6960  Score: 137
    Period size: 25  Copynumber: 4.0  Consensus size: 25

       6851 TGTGTTTTCC

                    *    *        *  
       6861 AAACGCAAGCACAAGCTCGTTTACT
          1 AAACGCAAACACAGGCTCGTTTGCT

                           *      * *
       6886 AAACGCAAACACAGGTTCGTTTTCC
          1 AAACGCAAACACAGGCTCGTTTGCT

                                     
       6911 AAACGCAAACACAGGCTCGTTTGCT
          1 AAACGCAAACACAGGCTCGTTTGCT

                    *                
       6936 AAACGCAAGCACAGGCTCGTTTGCT
          1 AAACGCAAACACAGGCTCGTTTGCT

       6961 CAGCGCACGC


Statistics
Matches: 66,  Mismatches: 9, Indels: 0
        0.88            0.12        0.00

Matches are distributed among these distances:
  25   66  1.00

ACGTcount: A:0.32, C:0.28, G:0.19, T:0.21


Consensus pattern (25 bp):   
AAACGCAAACACAGGCTCGTTTGCT

Found at i:11047 original size:32 final size:32

Alignment explanation


    Indices: 11011--11079  Score: 138
    Period size: 32  Copynumber: 2.2  Consensus size: 32

      11001 TCAGGGGGCG

                                            
      11011 CCTCCCACCGTGGCGGGGCGCCCCTGGGGACA
          1 CCTCCCACCGTGGCGGGGCGCCCCTGGGGACA

                                            
      11043 CCTCCCACCGTGGCGGGGCGCCCCTGGGGACA
          1 CCTCCCACCGTGGCGGGGCGCCCCTGGGGACA

                 
      11075 CCTCC
          1 CCTCC

      11080 GCGC


Statistics
Matches: 37,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  32   37  1.00

ACGTcount: A:0.09, C:0.46, G:0.35, T:0.10


Consensus pattern (32 bp):   
CCTCCCACCGTGGCGGGGCGCCCCTGGGGACA
Done.