Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Scaffold1235

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: 14644
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33


Found at i:10438 original size:20 final size:19

Alignment explanation


    Indices: 10412--10483  Score: 81
    Period size: 20  Copynumber: 3.6  Consensus size: 19

      10402 AAGACATAAC

                                
      10412 GTATCGATACATTGAAGAAT
          1 GTATCGATACATTGAA-AAT

            *            *   *  
      10432 ATATCGATACATTCATACAT
          1 GTATCGATACATTGA-AAAT

                     *          
      10452 GTATCGATATATTGAAAAAT
          1 GTATCGATACATTG-AAAAT

                        
      10472 GTATCGATACAT
          1 GTATCGATACAT

      10484 CTGGGTAAAA


Statistics
Matches: 42,  Mismatches: 8, Indels: 4
        0.78            0.15        0.07

Matches are distributed among these distances:
  20   40  0.95
  21    2  0.05

ACGTcount: A:0.40, C:0.12, G:0.14, T:0.33


Consensus pattern (19 bp):   
GTATCGATACATTGAAAAT

Found at i:13607 original size:3 final size:3

Alignment explanation


    Indices: 13599--13635  Score: 65
    Period size: 3  Copynumber: 12.0  Consensus size: 3

      13589 TTTATGTAAG

                                                            
      13599 AAT AAT AAT AAT AAT AAAT AAT AAT AAT AAT AAT AAT
          1 AAT AAT AAT AAT AAT -AAT AAT AAT AAT AAT AAT AAT

      13636 GACAATGATG


Statistics
Matches: 33,  Mismatches: 0, Indels: 2
        0.94            0.00        0.06

Matches are distributed among these distances:
   3   30  0.91
   4    3  0.09

ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32


Consensus pattern (3 bp):   
AAT

Found at i:14202 original size:20 final size:21

Alignment explanation


    Indices: 14177--14225  Score: 66
    Period size: 22  Copynumber: 2.4  Consensus size: 21

      14167 TTTTTAAAAA

                                 
      14177 ATTTAAA-TTATTTAATATAT
          1 ATTTAAATTTATTTAATATAT

                                  
      14197 ATTTAAATTTTATTTAATATA-
          1 ATTTAAA-TTTATTTAATATAT

              *     
      14218 ATATAAAT
          1 ATTTAAAT

      14226 AAATTTATAT


Statistics
Matches: 26,  Mismatches: 1, Indels: 4
        0.84            0.03        0.13

Matches are distributed among these distances:
  20    8  0.31
  21    6  0.23
  22   12  0.46

ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53


Consensus pattern (21 bp):   
ATTTAAATTTATTTAATATAT

Found at i:14231 original size:25 final size:22

Alignment explanation


    Indices: 14184--14225  Score: 68
    Period size: 22  Copynumber: 2.0  Consensus size: 22

      14174 AAAATTTAAA

                           *      
      14184 TTATTTAATATATATTTAAATT
          1 TTATTTAATATATATATAAATT

                                 
      14206 TTATTTAATATA-ATATAAAT
          1 TTATTTAATATATATATAAAT

      14226 AAATTTATAT


Statistics
Matches: 19,  Mismatches: 1, Indels: 1
        0.90            0.05        0.05

Matches are distributed among these distances:
  21    7  0.37
  22   12  0.63

ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55


Consensus pattern (22 bp):   
TTATTTAATATATATATAAATT
Done.