Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Scaffold393

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: 43382
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32


Found at i:4417 original size:94 final size:97

Alignment explanation


    Indices: 4319--4497  Score: 219
    Period size: 96  Copynumber: 1.9  Consensus size: 97

       4309 CAGACAACAA

                                                                 *  *        
       4319 GTTGACGCCATGT-C-CAGAC-GGTCTTACAACTAGCTTGTAT-ATC-TCAAGGGCCGAT-CATG
          1 GTTGACG-CATGTCCGCAGACAGGT-TTAC-ACTAGCTTGTATAATCTTCAA-AGCAGATGCATG

                                                
       4378 TCCCAGACATGTCTTAC-ACTAGCTCTCGTCTCAAT
         62 TCCCAGACATGTCTTACAACTAGCTCTCGTCTCAAT

                 *               *         *              *                  
       4413 GTTGATGCATGTCCGCAGACATGTTTACACTGGCTTGTATAATCTTGAAAGCAGATGCATGTCCC
          1 GTTGACGCATGTCCGCAGACAGGTTTACACTAGCTTGTATAATCTTCAAAGCAGATGCATGTCCC

                                
       4478 AGACATGTCTTACAACTAGC
         66 AGACATGTCTTACAACTAGC

       4498 ACACCCATAT


Statistics
Matches: 72,  Mismatches: 6, Indels: 11
        0.81            0.07        0.12

Matches are distributed among these distances:
  93    5  0.07
  94   18  0.25
  95   17  0.24
  96   26  0.36
  97    6  0.08

ACGTcount: A:0.25, C:0.26, G:0.20, T:0.29


Consensus pattern (97 bp):   
GTTGACGCATGTCCGCAGACAGGTTTACACTAGCTTGTATAATCTTCAAAGCAGATGCATGTCCC
AGACATGTCTTACAACTAGCTCTCGTCTCAAT

Found at i:33293 original size:29 final size:29

Alignment explanation


    Indices: 33260--33333  Score: 96
    Period size: 29  Copynumber: 2.6  Consensus size: 29

      33250 GTTGTGAGAT

                    *                  *  
      33260 TGGCACTAGGTGTGCGAACTTGAAA-TGCA
          1 TGGCACTAAGTGTGCG-ACTTGAAAGTACA

                             *  *        
      33289 TGGCACTAAGTGTGCGAGTTTAAAGTACA
          1 TGGCACTAAGTGTGCGACTTGAAAGTACA

                            
      33318 TGGCACTAAGTGTGCG
          1 TGGCACTAAGTGTGCG

      33334 TGGTTGATTA


Statistics
Matches: 40,  Mismatches: 4, Indels: 2
        0.87            0.09        0.04

Matches are distributed among these distances:
  28    6  0.15
  29   34  0.85

ACGTcount: A:0.27, C:0.16, G:0.31, T:0.26


Consensus pattern (29 bp):   
TGGCACTAAGTGTGCGACTTGAAAGTACA
Done.