Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Scaffold811

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: 7987
ACGTcount: A:0.29, C:0.25, G:0.17, T:0.29


Found at i:6219 original size:27 final size:27

Alignment explanation


    Indices: 6189--6366  Score: 205
    Period size: 27  Copynumber: 6.6  Consensus size: 27

       6179 ATATTGAGTC

                    *       *   *    * 
       6189 CGCACACTCAGTGCTATATAATCAACT
          1 CGCACACTTAGTGCTACATAGTCAAAT

                             *  *      
       6216 CGCACACTTAGTGCTACGTAATCAAAT
          1 CGCACACTTAGTGCTACATAGTCAAAT

                                        
       6243 CGCACACTTAGTGCTACATAGTCAAACT
          1 CGCACACTTAGTGCTACATAGTCAAA-T

                          **   *     * 
       6271 CGCACACTTAGTGCCGCATGGTCAATT
          1 CGCACACTTAGTGCTACATAGTCAAAT

                                 *   ** 
       6298 CGCACACTTAGTGC-ATCATATTCATTT
          1 CGCACACTTAGTGCTA-CATAGTCAAAT

                          *            
       6325 CGCACACTTAGTGCAACATAGTCAAAT
          1 CGCACACTTAGTGCTACATAGTCAAAT

                           
       6352 CGCACACTTAGTGCT
          1 CGCACACTTAGTGCT

       6367 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:6328 original size:82 final size:81

Alignment explanation


    Indices: 6210--6365  Score: 233
    Period size: 82  Copynumber: 1.9  Consensus size: 81

       6200 TGCTATATAA

                                   *                       *                 
       6210 TCAACTCGCACACTTAGTGCTACGTAATCAAATCGCACACTTAGTGCTACATAGTCAAACTCGCA
          1 TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAA-TCGCA

                             
       6275 CACTTAGTGCCGCATGG
         65 CACTTAGTGCCGCATGG

                *                      *   **                                
       6292 TCAATTCGCACACTTAGTGC-ATCATATTCATTTCGCACACTTAGTGCAACATAGTCAAATCGCA
          1 TCAACTCGCACACTTAGTGCTA-CATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCA

                      
       6356 CACTTAGTGC
         65 CACTTAGTGC

       6366 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.