Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: scaffold1195

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: 2396
ACGTcount: A:0.37, C:0.14, G:0.17, T:0.31


Found at i:432 original size:28 final size:27

Alignment explanation


    Indices: 401--488  Score: 83
    Period size: 28  Copynumber: 3.2  Consensus size: 27

        391 ATTTTTTAGT

                                        
        401 TATAATTATTTTAAATTTTATTAAATCA
          1 TATAATTATTTTAAATTTTATTAAAT-A

                             * *    *    
        429 TAT-ATT-TTAATTAAAATATATTTAATA
          1 TATAATTATT--TTAAATTTTATTAAATA

                       *                
        456 T-TAATTATTTCAAATTTTATTAAATTA
          1 TATAATTATTTTAAATTTTATTAAA-TA

                  
        483 TATAAT
          1 TATAAT

        489 ATAGTATCAT


Statistics
Matches: 47,  Mismatches: 7, Indels: 12
        0.71            0.11        0.18

Matches are distributed among these distances:
  26   14  0.30
  27   11  0.23
  28   22  0.47

ACGTcount: A:0.44, C:0.02, G:0.00, T:0.53


Consensus pattern (27 bp):   
TATAATTATTTTAAATTTTATTAAATA

Found at i:749 original size:40 final size:40

Alignment explanation


    Indices: 675--773  Score: 103
    Period size: 40  Copynumber: 2.5  Consensus size: 40

        665 GGCGCTTTAT

                 *          *     **      *          
        675 ATAAAACGCCGCTAATTC-CTATTTTTAGCGGCGCTTCCGG
          1 ATAAATCGCCGCTAATGCTCTACCTTTAGCAGCGCTT-CGG

                                                 *  
        715 AT-AATCGCCGCTAATGCTCTACCTTTAGCAGCGCTTTGG
          1 ATAAATCGCCGCTAATGCTCTACCTTTAGCAGCGCTTCGG

            *      *            
        754 CTAAATCACCGCTAATGCTC
          1 ATAAATCGCCGCTAATGCTC

        774 GATTTTTTGT


Statistics
Matches: 49,  Mismatches: 8, Indels: 4
        0.80            0.13        0.07

Matches are distributed among these distances:
  39   16  0.33
  40   33  0.67

ACGTcount: A:0.23, C:0.29, G:0.18, T:0.29


Consensus pattern (40 bp):   
ATAAATCGCCGCTAATGCTCTACCTTTAGCAGCGCTTCGG
Done.