Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: scaffold1334

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: 1995
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34


Found at i:478 original size:9 final size:8

Alignment explanation


    Indices: 449--483  Score: 52
    Period size: 8  Copynumber: 4.4  Consensus size: 8

        439 CTCAAAAGTC

                    
        449 AAAAAAGA
          1 AAAAAAGA

            *  *    
        457 GAAGAAGA
          1 AAAAAAGA

                    
        465 AAAAAAGA
          1 AAAAAAGA

                    
        473 AAAAAAGA
          1 AAAAAAGA

               
        481 AAA
          1 AAA

        484 CCCTTCGGTT


Statistics
Matches: 23,  Mismatches: 4, Indels: 0
        0.85            0.15        0.00

Matches are distributed among these distances:
   8   23  1.00

ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00


Consensus pattern (8 bp):   
AAAAAAGA

Found at i:1468 original size:16 final size:16

Alignment explanation


    Indices: 1447--1514  Score: 73
    Period size: 17  Copynumber: 4.1  Consensus size: 16

       1437 CATATTTTCA

                            
       1447 TTAAAAAATAAAAAAT
          1 TTAAAAAATAAAAAAT

                     *      
       1463 TTAAAAAATGAAAAAT
          1 TTAAAAAATAAAAAAT

               *            * 
       1479 TATGAAAAATAAAAATCT
          1 T-TAAAAAATAAAAA-AT

                     *       
       1497 TTAAAATAAAAAAAAAT
          1 TTAAAA-AATAAAAAAT

             
       1514 T
          1 T

       1515 GAAATGATTT


Statistics
Matches: 42,  Mismatches: 7, Indels: 5
        0.78            0.13        0.09

Matches are distributed among these distances:
  16   16  0.38
  17   17  0.40
  18    9  0.21

ACGTcount: A:0.69, C:0.01, G:0.03, T:0.26


Consensus pattern (16 bp):   
TTAAAAAATAAAAAAT

Found at i:1518 original size:33 final size:33

Alignment explanation


    Indices: 1450--1518  Score: 79
    Period size: 33  Copynumber: 2.1  Consensus size: 33

       1440 ATTTTCATTA

                                  *     *    
       1450 AAAAATAAAAAATTTAAAAAATGAAAAATTATG
          1 AAAAATAAAAAATTTAAAAAATAAAAAAATATG

                        *                      
       1483 AAAAATAAAAATCTTTAAAATAA-AAAAAAAT-TG
          1 AAAAATAAAAA-ATTTAAAA-AATAAAAAAATATG

               
       1516 AAA
          1 AAA

       1519 TGATTTTAAA


Statistics
Matches: 31,  Mismatches: 3, Indels: 4
        0.82            0.08        0.11

Matches are distributed among these distances:
  33   16  0.52
  34   13  0.42
  35    2  0.06

ACGTcount: A:0.71, C:0.01, G:0.04, T:0.23


Consensus pattern (33 bp):   
AAAAATAAAAAATTTAAAAAATAAAAAAATATG
Done.