Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: scaffold_734 ID=scaffold_734-JGI_221_v2.0

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: 4181
ACGTcount: A:0.39, C:0.10, G:0.19, T:0.31


Found at i:2162 original size:50 final size:50

Alignment explanation


    Indices: 2004--2333  Score: 278
    Period size: 50  Copynumber: 6.6  Consensus size: 50

       1994 CGATCTCGTA

                                     * *     * *   *            
       2004 TAAGACCATGTCTGGGACATGGCATCGACA-TCGATATGTGA-G--CCAGTG
          1 TAAGACCATGTCTGGGACATGGCATTGGCACT-AAGATGAGAGGTCCCA-TG

                                      *                           
       2052 TAAGACCATGTCTGGGACATGGCATTAGCA-TCACCGAGATGAGAGGTCCCATG
          1 TAAGACCATGTCTGGGACATGGCATTGGCACT-A---AGATGAGAGGTCCCATG

                                   *                          
       2105 TAAGACCATGTCTGGGACATGGCGTTGGCACTAAGATGAGAGGTCCCATG
          1 TAAGACCATGTCTGGGACATGGCATTGGCACTAAGATGAGAGGTCCCATG

                     *                     **               * 
       2155 TAAGACCATATCTGGGACATGGCATTGGCACCGAGATGAGAGGTCCCACG
          1 TAAGACCATGTCTGGGACATGGCATTGGCACTAAGATGAGAGGTCCCATG

            *             *    *     *     ** *      **   *   
       2205 GAAGACCATGTCTGCGACACGGCATGGGCACCGATATGAGAACTCCTATG
          1 TAAGACCATGTCTGGGACATGGCATTGGCACTAAGATGAGAGGTCCCATG

                     *       *            *         * **       
       2255 TAAGACCATATCTGGGATATGGCATTGGCAGTACAGA--AAACATCCCATG
          1 TAAGACCATGTCTGGGACATGGCATTGGCACTA-AGATGAGAGGTCCCATG

                  *             *  *      
       2304 TAAGACTATGTCTGGGACATAGCTTTGGCA
          1 TAAGACCATGTCTGGGACATGGCATTGGCA

       2334 TGTTATTATC


Statistics
Matches: 232,  Mismatches: 42, Indels: 15
        0.80            0.15        0.05

Matches are distributed among these distances:
  48   29  0.12
  49   33  0.14
  50  126  0.54
  51    8  0.03
  52    1  0.00
  53   31  0.13
  54    4  0.02

ACGTcount: A:0.28, C:0.22, G:0.28, T:0.22


Consensus pattern (50 bp):   
TAAGACCATGTCTGGGACATGGCATTGGCACTAAGATGAGAGGTCCCATG

Found at i:2212 original size:100 final size:100

Alignment explanation


    Indices: 2050--2284  Score: 308
    Period size: 100  Copynumber: 2.3  Consensus size: 100

       2040 TGTGAGCCAG

                       *                    *                    * *         
       2050 TGTAAGACCATGTCTGGGACATGGCATTAGCATCACCGAGATGAGAGGTCCCATGTAAGACCATG
          1 TGTAAGACCATATCTGGGACATGGCATT-G--GCACCGAGATGAGAGGTCCCACGGAAGACCATG

                *    *   * *     *         **     
       2115 TCTGGGACATGGCGTTGGCACTAAGATGAGAGGTCCCA
         63 TCTGCGACACGGCATGGGCACCAAGATGAGAACTCCCA

                                                                             
       2153 TGTAAGACCATATCTGGGACATGGCATTGGCACCGAGATGAGAGGTCCCACGGAAGACCATGTCT
          1 TGTAAGACCATATCTGGGACATGGCATTGGCACCGAGATGAGAGGTCCCACGGAAGACCATGTCT

                               * *           * 
       2218 GCGACACGGCATGGGCACCGATATGAGAACTCCTA
         66 GCGACACGGCATGGGCACCAAGATGAGAACTCCCA

                               *            
       2253 TGTAAGACCATATCTGGGATATGGCATTGGCA
          1 TGTAAGACCATATCTGGGACATGGCATTGGCA

       2285 GTACAGAAAA


Statistics
Matches: 117,  Mismatches: 15, Indels: 3
        0.87            0.11        0.02

Matches are distributed among these distances:
 100   89  0.76
 102    1  0.01
 103   27  0.23

ACGTcount: A:0.28, C:0.22, G:0.29, T:0.21


Consensus pattern (100 bp):   
TGTAAGACCATATCTGGGACATGGCATTGGCACCGAGATGAGAGGTCCCACGGAAGACCATGTCT
GCGACACGGCATGGGCACCAAGATGAGAACTCCCA
Done.