Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01009765.1 Corchorus olitorius cultivar O-4 contig09797, 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: 4180
ACGTcount: A:0.33, C:0.17, G:0.19, T:0.31


Found at i:2382 original size:10 final size:10

Alignment explanation


    Indices: 2367--2416  Score: 91
    Period size: 10  Copynumber: 5.0  Consensus size: 10

       2357 TTGAGCTTGG

                      
       2367 ACCTTTGGGC
          1 ACCTTTGGGC

                      
       2377 ACCTTTGGGC
          1 ACCTTTGGGC

                      
       2387 ACCTTTGGGC
          1 ACCTTTGGGC

                      
       2397 ACCTTTGGGC
          1 ACCTTTGGGC

              *       
       2407 ACATTTGGGC
          1 ACCTTTGGGC

       2417 TTAGAAGGGT


Statistics
Matches: 39,  Mismatches: 1, Indels: 0
        0.98            0.03        0.00

Matches are distributed among these distances:
  10   39  1.00

ACGTcount: A:0.12, C:0.28, G:0.30, T:0.30


Consensus pattern (10 bp):   
ACCTTTGGGC

Found at i:3398 original size:35 final size:35

Alignment explanation


    Indices: 3321--3488  Score: 137
    Period size: 35  Copynumber: 4.7  Consensus size: 35

       3311 TCAGTCTTCG

                   *   *               *  *    
       3321 AAGTTTTCAAATTGGGAAAGTTCCCACCAGGTTTT
          1 AAGTTTTTAAAATGGGAAAGTTCCCACAAGTTTTT

                          *                     
       3356 -AGTTTTTAAAATGAGAAAGTTCCCAACAAGTTTTT
          1 AAGTTTTTAAAATGGGAAAGTTCCC-ACAAGTTTTT

                               *        *       
       3391 AAG-TTTTAAAATTGGGAAGGTTCCCACCAGTTTTT
          1 AAGTTTTTAAAA-TGGGAAAGTTCCCACAAGTTTTT

                         *     *             *    
       3426 CAAAGTTTTTAAAGTGGGAGAGTTCCCATC-AGGTTTT
          1 --AAGTTTTTAAAATGGGAAAGTTCCCA-CAAGTTTTT

                   *  **               
       3463 -AGTTTTCAATTTAGGGAAAGTTCCCA
          1 AAGTTTTTAAAAT-GGGAAAGTTCCCA

       3489 TCATTTTCAG


Statistics
Matches: 109,  Mismatches: 16, Indels: 16
        0.77            0.11        0.11

Matches are distributed among these distances:
  34   30  0.28
  35   37  0.34
  36   13  0.12
  37   21  0.19
  38    8  0.07

ACGTcount: A:0.30, C:0.14, G:0.20, T:0.36


Consensus pattern (35 bp):   
AAGTTTTTAAAATGGGAAAGTTCCCACAAGTTTTT

Found at i:3491 original size:35 final size:35

Alignment explanation


    Indices: 3321--3488  Score: 169
    Period size: 34  Copynumber: 4.7  Consensus size: 35

       3311 TCAGTCTTCG

                                               
       3321 AAGTTTTCAAATTGGGAAAGTTCCCACCAGGTTTT
          1 AAGTTTTCAAATTGGGAAAGTTCCCACCAGGTTTT

                   *   *  *             *  *    
       3356 -AGTTTTTAAAATGAGAAAGTTCCCAACAAGTTTTT
          1 AAGTTTTCAAATTGGGAAAGTTCCC-ACCAGGTTTT

                   *          *           *    
       3391 AAGTTTTAAAATTGGGAAGGTTCCCACCAGTTTTT
          1 AAGTTTTCAAATTGGGAAAGTTCCCACCAGGTTTT

                     *   *     *        *        
       3426 CAAAGTTTTTAAAGTGGGAGAGTTCCCATCAGGTTTT
          1 --AAGTTTTCAAATTGGGAAAGTTCCCACCAGGTTTT

                      *                
       3463 -AGTTTTCAATTTAGGGAAAGTTCCCA
          1 AAGTTTTCAAATT-GGGAAAGTTCCCA

       3489 TCATTTTCAG


Statistics
Matches: 108,  Mismatches: 20, Indels: 10
        0.78            0.14        0.07

Matches are distributed among these distances:
  34   30  0.28
  35   29  0.27
  36   20  0.19
  37   29  0.27

ACGTcount: A:0.30, C:0.14, G:0.20, T:0.36


Consensus pattern (35 bp):   
AAGTTTTCAAATTGGGAAAGTTCCCACCAGGTTTT
Done.