Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Scaffold1715

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: 17366
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.34


Found at i:532 original size:2 final size:2

Alignment explanation


    Indices: 525--555  Score: 62
    Period size: 2  Copynumber: 15.5  Consensus size: 2

        515 ACACATACAA

                                                          
        525 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
          1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A

        556 ATGAAGGATC


Statistics
Matches: 29,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   29  1.00

ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48


Consensus pattern (2 bp):   
AT

Found at i:1092 original size:20 final size:20

Alignment explanation


    Indices: 1051--1092  Score: 57
    Period size: 20  Copynumber: 2.1  Consensus size: 20

       1041 GTCATAAAAT

                           * *  
       1051 GAAAAAGACAATATATATGA
          1 GAAAAAGACAATATAAAAGA

                 *              
       1071 GAAAATGACAATATAAAAGA
          1 GAAAAAGACAATATAAAAGA

              
       1091 GA
          1 GA

       1093 TTTTGAGAAA


Statistics
Matches: 19,  Mismatches: 3, Indels: 0
        0.86            0.14        0.00

Matches are distributed among these distances:
  20   19  1.00

ACGTcount: A:0.62, C:0.05, G:0.17, T:0.17


Consensus pattern (20 bp):   
GAAAAAGACAATATAAAAGA

Found at i:2153 original size:17 final size:20

Alignment explanation


    Indices: 2131--2170  Score: 59
    Period size: 20  Copynumber: 2.1  Consensus size: 20

       2121 ATCTTAGTTA

                                
       2131 TAAATA-TT-AAA-GAATAT
          1 TAAATATTTAAAAGGAATAT

                                
       2148 TAAATATTTAAAAGGAATAT
          1 TAAATATTTAAAAGGAATAT

               
       2168 TAA
          1 TAA

       2171 TTTGGTCTAA


Statistics
Matches: 20,  Mismatches: 0, Indels: 3
        0.87            0.00        0.13

Matches are distributed among these distances:
  17    6  0.30
  18    2  0.10
  19    3  0.15
  20    9  0.45

ACGTcount: A:0.57, C:0.00, G:0.07, T:0.35


Consensus pattern (20 bp):   
TAAATATTTAAAAGGAATAT

Found at i:14863 original size:6 final size:6

Alignment explanation


    Indices: 14852--14877  Score: 52
    Period size: 6  Copynumber: 4.3  Consensus size: 6

      14842 GCATGAACAG

                                          
      14852 CAGCAA CAGCAA CAGCAA CAGCAA CA
          1 CAGCAA CAGCAA CAGCAA CAGCAA CA

      14878 AAGATTGGAA


Statistics
Matches: 20,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   6   20  1.00

ACGTcount: A:0.50, C:0.35, G:0.15, T:0.00


Consensus pattern (6 bp):   
CAGCAA

Done.