Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: evm.model.Scaffold412.330

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: 4395
ACGTcount: A:0.27, C:0.24, G:0.22, T:0.27


Found at i:2346 original size:51 final size:51

Alignment explanation


    Indices: 2305--2418  Score: 192
    Period size: 51  Copynumber: 2.2  Consensus size: 51

       2295 TCCGCCACCC

                       *                                       
       2305 CCACCTCCACCTCCACCACCATTGCCTCCTGGTCACAGAGCTTCTCCTCCA
          1 CCACCTCCACCACCACCACCATTGCCTCCTGGTCACAGAGCTTCTCCTCCA

                                               **             *
       2356 CCACCTCCACCACCACCACCATTGCCTCCTGGTCATGGAGCTTCTCCTCCT
          1 CCACCTCCACCACCACCACCATTGCCTCCTGGTCACAGAGCTTCTCCTCCA

                        
       2407 CCACCTCCACCA
          1 CCACCTCCACCA

       2419 TTACCTCTTG


Statistics
Matches: 59,  Mismatches: 4, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
  51   59  1.00

ACGTcount: A:0.18, C:0.52, G:0.10, T:0.21


Consensus pattern (51 bp):   
CCACCTCCACCACCACCACCATTGCCTCCTGGTCACAGAGCTTCTCCTCCA

Found at i:2354 original size:42 final size:42

Alignment explanation


    Indices: 2308--2463  Score: 123
    Period size: 51  Copynumber: 3.4  Consensus size: 42

       2298 GCCACCCCCA

                                             *        
       2308 CCTCCACCTCCACCACCATTGCCTCCTGGTCACAGAGCTTCT
          1 CCTCCACCTCCACCACCATTGCCTCCTGGTCACGGAGCTTCT

                                                     *         
       2350 CCTCCACCACCTCCACCACCACCACCATTGCCTCCTGGTCATGGAGCTTCT
          1 CCT---CCACCT------CCACCACCATTGCCTCCTGGTCACGGAGCTTCT

                 *  *  *        *    *   * *             
       2401 CCTCCTCCACCTCCACCATTACCTCTTGGCCGCGGAGCTTCTCCT
          1 CCTCCACCTCCACCACCATTGCCTCCTGGTCACGGAGC-T-T-CT

                              
       2446 CCTCCACCTCCACCACCA
          1 CCTCCACCTCCACCACCA

       2464 CCTCTTTTAC


Statistics
Matches: 89,  Mismatches: 13, Indels: 21
        0.72            0.11        0.17

Matches are distributed among these distances:
  42   26  0.29
  43    1  0.01
  44    1  0.01
  45   23  0.26
  48    4  0.04
  51   34  0.38

ACGTcount: A:0.16, C:0.51, G:0.11, T:0.22


Consensus pattern (42 bp):   
CCTCCACCTCCACCACCATTGCCTCCTGGTCACGGAGCTTCT

Found at i:2674 original size:39 final size:39

Alignment explanation


    Indices: 2604--2706  Score: 158
    Period size: 39  Copynumber: 2.7  Consensus size: 39

       2594 CTCCCCGACA

                              *                    
       2604 TGGAGCACCA-C-CC-CCACCACCTCCTCCACCTGTTCG
          1 TGGAGCACCAGCACCACCCCCACCTCCTCCACCTGTTCG

                 **                                
       2640 TGGAGTGCCAGCACCACCCCCACCTCCTCCACCTGTTCG
          1 TGGAGCACCAGCACCACCCCCACCTCCTCCACCTGTTCG

                                        
       2679 TGGAGCACCAGCACCACCCCCACCTCCT
          1 TGGAGCACCAGCACCACCCCCACCTCCT

       2707 ATGTGTGGAG


Statistics
Matches: 59,  Mismatches: 5, Indels: 3
        0.88            0.07        0.04

Matches are distributed among these distances:
  36    8  0.14
  37    1  0.02
  38    2  0.03
  39   48  0.81

ACGTcount: A:0.17, C:0.51, G:0.16, T:0.16


Consensus pattern (39 bp):   
TGGAGCACCAGCACCACCCCCACCTCCTCCACCTGTTCG

Done.