Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: scaffold1504

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, 979

Length: 1633
ACGTcount: A:0.36, C:0.14, G:0.13, T:0.37


Found at i:1593 original size:21 final size:21

Alignment explanation


    Indices: 1567--1606  Score: 64
    Period size: 21  Copynumber: 1.9  Consensus size: 21

       1557 ATGTGTTTTT

                                  
       1567 ATTTATT-TATATATTTTTTAA
          1 ATTTATTAT-TATATTTTTTAA

                               
       1588 ATTTATTATTATATTTTTT
          1 ATTTATTATTATATTTTTT

       1607 TGAAAATATT


Statistics
Matches: 18,  Mismatches: 0, Indels: 2
        0.90            0.00        0.10

Matches are distributed among these distances:
  21   17  0.94
  22    1  0.06

ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70


Consensus pattern (21 bp):   
ATTTATTATTATATTTTTTAA

Found at i:1616 original size:22 final size:23

Alignment explanation


    Indices: 1573--1616  Score: 56
    Period size: 22  Copynumber: 2.0  Consensus size: 23

       1563 TTTTATTTAT

                             *     
       1573 TTATATATTTTTTAAATTTATTA
          1 TTATATATTTTTTAAATATATTA

                                   
       1596 TTATAT-TTTTTTGAAA-ATATT
          1 TTATATATTTTTT-AAATATATT

       1617 TATGTATTTT


Statistics
Matches: 19,  Mismatches: 1, Indels: 3
        0.83            0.04        0.13

Matches are distributed among these distances:
  22   10  0.53
  23    9  0.47

ACGTcount: A:0.34, C:0.00, G:0.02, T:0.64


Consensus pattern (23 bp):   
TTATATATTTTTTAAATATATTA

Found at i:1619 original size:23 final size:21

Alignment explanation


    Indices: 1566--1627  Score: 54
    Period size: 22  Copynumber: 2.8  Consensus size: 21

       1556 TATGTGTTTT

                                   
       1566 TATTTATTTATATATTTTTTAAA
          1 TATTTA-TTATAT-TTTTTTAAA

             *                      
       1589 TTTATTATTATATTTTTTTGAAAA
          1 TAT-TTATTATATTTTTTT--AAA

                    *       
       1613 TATTTA-TGTATTTTT
          1 TATTTATTATATTTTT

       1628 ATATAT


Statistics
Matches: 33,  Mismatches: 3, Indels: 7
        0.77            0.07        0.16

Matches are distributed among these distances:
  22   14  0.42
  23   11  0.33
  24    8  0.24

ACGTcount: A:0.31, C:0.00, G:0.03, T:0.66


Consensus pattern (21 bp):   
TATTTATTATATTTTTTTAAA
Done.