Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Scaffold1383

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: 18787
ACGTcount: A:0.35, C:0.18, G:0.18, T:0.30


Found at i:12895 original size:95 final size:94

Alignment explanation


    Indices: 12733--12922  Score: 353
    Period size: 95  Copynumber: 2.0  Consensus size: 94

      12723 AAAGGAATAG

                                                                             
      12733 CAAAACAATTGGGTGCAAGCCATCATGAGATAATGCAAAAGTAAATATAACAAGATCAAAATGGC
          1 CAAAACAATTGGGTGCAAGCCATCATGAGATAATGCAAAAGTAAATATAACAAGATCAAAATGGC

                                         
      12798 TAAATAGCATTATTTAGTTGTCAGTTCGA
         66 TAAATAGCATTATTTAGTTGTCAGTTCGA

                                                *                 *          
      12827 CAAAACAATTGGGGTGCAAGCCATCATGAGATAATGTAAAAGTAAATATAACAATATCAAAATGG
          1 CAAAACAATT-GGGTGCAAGCCATCATGAGATAATGCAAAAGTAAATATAACAAGATCAAAATGG

                                          
      12892 CTAAATAGCATTATTTAGTTGTCAGTTCGA
         65 CTAAATAGCATTATTTAGTTGTCAGTTCGA

             
      12922 C
          1 C

      12923 TAAGGAGATT


Statistics
Matches: 93,  Mismatches: 2, Indels: 1
        0.97            0.02        0.01

Matches are distributed among these distances:
  94   10  0.11
  95   83  0.89

ACGTcount: A:0.42, C:0.14, G:0.18, T:0.26


Consensus pattern (94 bp):   
CAAAACAATTGGGTGCAAGCCATCATGAGATAATGCAAAAGTAAATATAACAAGATCAAAATGGC
TAAATAGCATTATTTAGTTGTCAGTTCGA

Found at i:18678 original size:15 final size:14

Alignment explanation


    Indices: 18634--18681  Score: 60
    Period size: 15  Copynumber: 3.3  Consensus size: 14

      18624 AATGGTATAA

                          
      18634 TTTAAAATTTAATT
          1 TTTAAAATTTAATT

            *    *         
      18648 CTTAACATTTATATT
          1 TTTAAAATTTA-ATT

                           
      18663 TTTAATAATTTAATT
          1 TTTAA-AATTTAATT

                
      18678 TTTA
          1 TTTA

      18682 TTTTTATTAA


Statistics
Matches: 28,  Mismatches: 4, Indels: 3
        0.80            0.11        0.09

Matches are distributed among these distances:
  14    9  0.32
  15   14  0.50
  16    5  0.18

ACGTcount: A:0.38, C:0.04, G:0.00, T:0.58


Consensus pattern (14 bp):   
TTTAAAATTTAATT

Found at i:18686 original size:22 final size:23

Alignment explanation


    Indices: 18655--18716  Score: 65
    Period size: 23  Copynumber: 2.7  Consensus size: 23

      18645 ATTCTTAACA

                                   *
      18655 TTTATATTTTTAAT-AATTTAATT
          1 TTTAT-TTTTTAATAAATTTAATC

                       *       *   
      18678 TTTA-TTTTTATTAAATTTGATC
          1 TTTATTTTTTAATAAATTTAATC

                        *    
      18700 TTTATTTTTTAAAAAAT
          1 TTTATTTTTTAATAAAT

      18717 AATTGAATAT


Statistics
Matches: 32,  Mismatches: 5, Indels: 4
        0.78            0.12        0.10

Matches are distributed among these distances:
  21    7  0.22
  22   11  0.34
  23   14  0.44

ACGTcount: A:0.34, C:0.02, G:0.02, T:0.63


Consensus pattern (23 bp):   
TTTATTTTTTAATAAATTTAATC

Done.