Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Scaffold2863

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: 62676
ACGTcount: A:0.35, C:0.16, G:0.15, T:0.34


Found at i:32466 original size:23 final size:23

Alignment explanation


    Indices: 32440--32537  Score: 162
    Period size: 23  Copynumber: 4.3  Consensus size: 23

      32430 ATAAGTGCCA

                                   
      32440 CACTGATATGTAGCCGAAGCTAC
          1 CACTGATATGTAGCCGAAGCTAC

                                   
      32463 CACTGATATGTAGCCGAAGCTAC
          1 CACTGATATGTAGCCGAAGCTAC

                  *        *       
      32486 CACTG-GATGTAGCCAAAGCTAC
          1 CACTGATATGTAGCCGAAGCTAC

                  *                
      32508 CACTGAAATGTAGCCGAAGCTAC
          1 CACTGATATGTAGCCGAAGCTAC

                   
      32531 CACTGAT
          1 CACTGAT

      32538 CAATAACACT


Statistics
Matches: 69,  Mismatches: 5, Indels: 2
        0.91            0.07        0.03

Matches are distributed among these distances:
  22   20  0.29
  23   49  0.71

ACGTcount: A:0.32, C:0.27, G:0.21, T:0.20


Consensus pattern (23 bp):   
CACTGATATGTAGCCGAAGCTAC

Found at i:32505 original size:45 final size:45

Alignment explanation


    Indices: 32447--32535  Score: 160
    Period size: 45  Copynumber: 2.0  Consensus size: 45

      32437 CCACACTGAT

                    *             *                      
      32447 ATGTAGCCGAAGCTACCACTGATATGTAGCCGAAGCTACCACTGG
          1 ATGTAGCCAAAGCTACCACTGAAATGTAGCCGAAGCTACCACTGG

                                                        
      32492 ATGTAGCCAAAGCTACCACTGAAATGTAGCCGAAGCTACCACTG
          1 ATGTAGCCAAAGCTACCACTGAAATGTAGCCGAAGCTACCACTG

      32536 ATCAATAACA


Statistics
Matches: 42,  Mismatches: 2, Indels: 0
        0.95            0.05        0.00

Matches are distributed among these distances:
  45   42  1.00

ACGTcount: A:0.31, C:0.27, G:0.22, T:0.19


Consensus pattern (45 bp):   
ATGTAGCCAAAGCTACCACTGAAATGTAGCCGAAGCTACCACTGG

Found at i:39353 original size:23 final size:23

Alignment explanation


    Indices: 39327--39423  Score: 162
    Period size: 23  Copynumber: 4.3  Consensus size: 23

      39317 ATAAGTGCCA

                                   
      39327 CACTGATATGTAGCCGAAGCTAC
          1 CACTGATATGTAGCCGAAGCTAC

                                   
      39350 CACTGATATGTAGCCGAAGCTAC
          1 CACTGATATGTAGCCGAAGCTAC

                           *       
      39373 CACTG--ATGTAGCCAAAGCTAC
          1 CACTGATATGTAGCCGAAGCTAC

                  *                
      39394 CACTGAAATGTAGCCGAAGCTAC
          1 CACTGATATGTAGCCGAAGCTAC

                   
      39417 CACTGAT
          1 CACTGAT

      39424 CAATAACACT


Statistics
Matches: 69,  Mismatches: 3, Indels: 4
        0.91            0.04        0.05

Matches are distributed among these distances:
  21   20  0.29
  23   49  0.71

ACGTcount: A:0.32, C:0.27, G:0.21, T:0.21


Consensus pattern (23 bp):   
CACTGATATGTAGCCGAAGCTAC

Found at i:39392 original size:44 final size:44

Alignment explanation


    Indices: 39334--39423  Score: 162
    Period size: 44  Copynumber: 2.0  Consensus size: 44

      39324 CCACACTGAT

                    *             *                     
      39334 ATGTAGCCGAAGCTACCACTGATATGTAGCCGAAGCTACCACTG
          1 ATGTAGCCAAAGCTACCACTGAAATGTAGCCGAAGCTACCACTG

                                                        
      39378 ATGTAGCCAAAGCTACCACTGAAATGTAGCCGAAGCTACCACTG
          1 ATGTAGCCAAAGCTACCACTGAAATGTAGCCGAAGCTACCACTG

              
      39422 AT
          1 AT

      39424 CAATAACACT


Statistics
Matches: 44,  Mismatches: 2, Indels: 0
        0.96            0.04        0.00

Matches are distributed among these distances:
  44   44  1.00

ACGTcount: A:0.32, C:0.27, G:0.21, T:0.20


Consensus pattern (44 bp):   
ATGTAGCCAAAGCTACCACTGAAATGTAGCCGAAGCTACCACTG
Done.