Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: scaffold_5847

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: 9527
ACGTcount: A:0.28, C:0.24, G:0.18, T:0.30


Found at i:2496 original size:27 final size:27

Alignment explanation


    Indices: 2466--2643  Score: 205
    Period size: 27  Copynumber: 6.6  Consensus size: 27

       2456 ATATTGAGTC

                    *       *   *    * 
       2466 CGCACACTCAGTGCTATATAATCAACT
          1 CGCACACTTAGTGCTACATAGTCAAAT

                             *  *      
       2493 CGCACACTTAGTGCTACGTAATCAAAT
          1 CGCACACTTAGTGCTACATAGTCAAAT

                                        
       2520 CGCACACTTAGTGCTACATAGTCAAACT
          1 CGCACACTTAGTGCTACATAGTCAAA-T

                          **   *     * 
       2548 CGCACACTTAGTGCCGCATGGTCAATT
          1 CGCACACTTAGTGCTACATAGTCAAAT

                                 *   ** 
       2575 CGCACACTTAGTGC-ATCATATTCATTT
          1 CGCACACTTAGTGCTA-CATAGTCAAAT

                          *            
       2602 CGCACACTTAGTGCAACATAGTCAAAT
          1 CGCACACTTAGTGCTACATAGTCAAAT

                           
       2629 CGCACACTTAGTGCT
          1 CGCACACTTAGTGCT

       2644 GTACAATTTA


Statistics
Matches: 130,  Mismatches: 18, Indels: 6
        0.84            0.12        0.04

Matches are distributed among these distances:
  27  106  0.82
  28   24  0.18

ACGTcount: A:0.30, C:0.28, G:0.15, T:0.27


Consensus pattern (27 bp):   
CGCACACTTAGTGCTACATAGTCAAAT

Found at i:2605 original size:82 final size:81

Alignment explanation


    Indices: 2487--2642  Score: 233
    Period size: 82  Copynumber: 1.9  Consensus size: 81

       2477 TGCTATATAA

                                   *                       *                 
       2487 TCAACTCGCACACTTAGTGCTACGTAATCAAATCGCACACTTAGTGCTACATAGTCAAACTCGCA
          1 TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAA-TCGCA

                             
       2552 CACTTAGTGCCGCATGG
         65 CACTTAGTGCCGCATGG

                *                      *   **                                
       2569 TCAATTCGCACACTTAGTGC-ATCATATTCATTTCGCACACTTAGTGCAACATAGTCAAATCGCA
          1 TCAACTCGCACACTTAGTGCTA-CATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCA

                      
       2633 CACTTAGTGC
         65 CACTTAGTGC

       2643 TGTACAATTT


Statistics
Matches: 67,  Mismatches: 6, Indels: 3
        0.88            0.08        0.04

Matches are distributed among these distances:
  81   16  0.24
  82   51  0.76

ACGTcount: A:0.29, C:0.28, G:0.15, T:0.27


Consensus pattern (81 bp):   
TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCAC
ACTTAGTGCCGCATGG

Done.