Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01023949.1 Corchorus olitorius cultivar O-4 contig23982, 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: 8623
ACGTcount: A:0.32, C:0.16, G:0.20, T:0.32


Found at i:2138 original size:27 final size:27

Alignment explanation


    Indices: 2100--2185  Score: 122
    Period size: 27  Copynumber: 3.2  Consensus size: 27

       2090 AGCTTAAAAC

                           *           
       2100 GACCAAAATGCCCCTGGACGTGCAAAT
          1 GACCAAAATGCCCCTAGACGTGCAAAT

                                       
       2127 GACCAAAATGCCCCTAGACGTGCAAAT
          1 GACCAAAATGCCCCTAGACGTGCAAAT

                               *   *    
       2154 GA-CAATAATGCCCCTAGATGTGTAAAT
          1 GACCAA-AATGCCCCTAGACGTGCAAAT

                  
       2181 G-CCAA
          1 GACCAA

       2186 TTAAGAAATG


Statistics
Matches: 54,  Mismatches: 3, Indels: 4
        0.89            0.05        0.07

Matches are distributed among these distances:
  26    3  0.06
  27   51  0.94

ACGTcount: A:0.36, C:0.27, G:0.20, T:0.17


Consensus pattern (27 bp):   
GACCAAAATGCCCCTAGACGTGCAAAT

Found at i:6750 original size:27 final size:27

Alignment explanation


    Indices: 6719--6795  Score: 118
    Period size: 27  Copynumber: 2.9  Consensus size: 27

       6709 AAGTGAACTT

                   *                   
       6719 AAATGACCAAAATGCCCCTGAATATGC
          1 AAATGACTAAAATGCCCCTGAATATGC

                                * *    
       6746 AAATGACTAAAATGCCCCTGGACATGC
          1 AAATGACTAAAATGCCCCTGAATATGC

                     *             
       6773 AAATGACTACAATGCCCCTGAAT
          1 AAATGACTAAAATGCCCCTGAAT

       6796 GACTTAAGTG


Statistics
Matches: 44,  Mismatches: 6, Indels: 0
        0.88            0.12        0.00

Matches are distributed among these distances:
  27   44  1.00

ACGTcount: A:0.39, C:0.26, G:0.16, T:0.19


Consensus pattern (27 bp):   
AAATGACTAAAATGCCCCTGAATATGC

Found at i:7227 original size:42 final size:42

Alignment explanation


    Indices: 7176--7263  Score: 106
    Period size: 42  Copynumber: 2.1  Consensus size: 42

       7166 TTGATATAGG

                      *   *  *  *                      
       7176 TCATACATCCTTCATGCGTTGTCCATGT-CTTTGTATATATGT
          1 TCATACATCCATCAGGCATTATCCAT-TCCTTTGTATATATGT

                                  **                  
       7218 TCATACATCCATCAGGCATTATTGATTCCTTTGTATATATGT
          1 TCATACATCCATCAGGCATTATCCATTCCTTTGTATATATGT

                
       7260 TCAT
          1 TCAT

       7264 GCATAGGTCA


Statistics
Matches: 39,  Mismatches: 6, Indels: 2
        0.83            0.13        0.04

Matches are distributed among these distances:
  41    1  0.03
  42   38  0.97

ACGTcount: A:0.23, C:0.20, G:0.12, T:0.44


Consensus pattern (42 bp):   
TCATACATCCATCAGGCATTATCCATTCCTTTGTATATATGT

Found at i:8455 original size:16 final size:15

Alignment explanation


    Indices: 8437--8472  Score: 56
    Period size: 15  Copynumber: 2.5  Consensus size: 15

       8427 CAAGACATGT

                           
       8437 TTTTCAAGAAAATTG
          1 TTTTCAAGAAAATTG

                         * 
       8452 TTTTCAAGAAAA-AG
          1 TTTTCAAGAAAATTG

                   
       8466 TTTTCAA
          1 TTTTCAA

       8473 AAATAGGTTT


Statistics
Matches: 20,  Mismatches: 1, Indels: 1
        0.91            0.05        0.05

Matches are distributed among these distances:
  14    8  0.40
  15   12  0.60

ACGTcount: A:0.42, C:0.08, G:0.11, T:0.39


Consensus pattern (15 bp):   
TTTTCAAGAAAATTG

Found at i:8470 original size:14 final size:13

Alignment explanation


    Indices: 8437--8496  Score: 66
    Period size: 14  Copynumber: 4.3  Consensus size: 13

       8427 CAAGACATGT

                         * 
       8437 TTTTCAAGAAAATTG
          1 TTTTCAA-AAAA-GG

                        * 
       8452 TTTTCAAGAAAAAG
          1 TTTTCAA-AAAAGG

                          
       8466 TTTTCAAAAATAGG
          1 TTTTCAAAAA-AGG

                         
       8480 TTTTCAAAAAAGG
          1 TTTTCAAAAAAGG

                
       8493 TTTT
          1 TTTT

       8497 GAGTCTTTTT


Statistics
Matches: 42,  Mismatches: 2, Indels: 4
        0.88            0.04        0.08

Matches are distributed among these distances:
  13   10  0.24
  14   20  0.48
  15   12  0.29

ACGTcount: A:0.42, C:0.07, G:0.13, T:0.38


Consensus pattern (13 bp):   
TTTTCAAAAAAGG
Done.