Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Scaffold3387

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: 3130
ACGTcount: A:0.33, C:0.21, G:0.15, T:0.31


Found at i:2216 original size:23 final size:23

Alignment explanation


    Indices: 2187--2283  Score: 153
    Period size: 23  Copynumber: 4.3  Consensus size: 23

       2177 ATAAGTGCCA

                                   
       2187 CACTGATATGTAGCCGAAGCTAC
          1 CACTGATATGTAGCCGAAGCTAC

                                   
       2210 CACTGATATGTAGCCGAAGCT-C
          1 CACTGATATGTAGCCGAAGCTAC

                  *        *       
       2232 CACTG-GATGTAGCCAAAGCTAC
          1 CACTGATATGTAGCCGAAGCTAC

                  *                
       2254 CACTGAAATGTAGCCGAAGCTAC
          1 CACTGATATGTAGCCGAAGCTAC

                   
       2277 CACTGAT
          1 CACTGAT

       2284 CAATAACACT


Statistics
Matches: 67,  Mismatches: 5, Indels: 4
        0.88            0.07        0.05

Matches are distributed among these distances:
  21   13  0.19
  22   12  0.18
  23   42  0.63

ACGTcount: A:0.31, C:0.27, G:0.22, T:0.21


Consensus pattern (23 bp):   
CACTGATATGTAGCCGAAGCTAC

Found at i:2251 original size:44 final size:45

Alignment explanation


    Indices: 2194--2281  Score: 151
    Period size: 44  Copynumber: 2.0  Consensus size: 45

       2184 CCACACTGAT

                    *             *                      
       2194 ATGTAGCCGAAGCTACCACTGATATGTAGCCGAAGCT-CCACTGG
          1 ATGTAGCCAAAGCTACCACTGAAATGTAGCCGAAGCTACCACTGG

                                                        
       2238 ATGTAGCCAAAGCTACCACTGAAATGTAGCCGAAGCTACCACTG
          1 ATGTAGCCAAAGCTACCACTGAAATGTAGCCGAAGCTACCACTG

       2282 ATCAATAACA


Statistics
Matches: 41,  Mismatches: 2, Indels: 1
        0.93            0.05        0.02

Matches are distributed among these distances:
  44   35  0.85
  45    6  0.15

ACGTcount: A:0.31, C:0.27, G:0.23, T:0.19


Consensus pattern (45 bp):   
ATGTAGCCAAAGCTACCACTGAAATGTAGCCGAAGCTACCACTGG
Done.