Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Scaffold1610

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: 159875
ACGTcount: A:0.31, C:0.18, G:0.20, T:0.31


File 2 of 2

Found at i:155413 original size:26 final size:26

Alignment explanation


    Indices: 155384--155433  Score: 91
    Period size: 26  Copynumber: 1.9  Consensus size: 26

     155374 AATGATGTAT

                           *          
     155384 GATGATATTATGAATGTATGATGCGA
          1 GATGATATTATGAATATATGATGCGA

                                    
     155410 GATGATATTATGAATATATGATGC
          1 GATGATATTATGAATATATGATGC

     155434 AGAATGCTAT


Statistics
Matches: 23,  Mismatches: 1, Indels: 0
        0.96            0.04        0.00

Matches are distributed among these distances:
  26   23  1.00

ACGTcount: A:0.36, C:0.04, G:0.24, T:0.36


Consensus pattern (26 bp):   
GATGATATTATGAATATATGATGCGA

Found at i:156466 original size:12 final size:11

Alignment explanation


    Indices: 156441--156494  Score: 72
    Period size: 11  Copynumber: 4.7  Consensus size: 11

     156431 ATCTGGACCC

                        
     156441 TTTTTTTGTTTG
          1 TTTTTTT-TTTG

                        
     156453 TTTGTTTTTTTG
          1 TTT-TTTTTTTG

               *     * 
     156465 TTTGTTTTTGG
          1 TTTTTTTTTTG

                       
     156476 TTTTTTTTTTG
          1 TTTTTTTTTTG

                    
     156487 TTTTTTTT
          1 TTTTTTTT

     156495 GTATGAAGGA


Statistics
Matches: 37,  Mismatches: 4, Indels: 3
        0.84            0.09        0.07

Matches are distributed among these distances:
  11   23  0.62
  12   10  0.27
  13    4  0.11

ACGTcount: A:0.00, C:0.00, G:0.15, T:0.85


Consensus pattern (11 bp):   
TTTTTTTTTTG

Found at i:156490 original size:8 final size:8

Alignment explanation


    Indices: 156441--156493  Score: 56
    Period size: 8  Copynumber: 6.9  Consensus size: 8

     156431 ATCTGGACCC

                    
     156441 TTTTTTTG
          1 TTTTTTTG

               *    
     156449 TTTGTTTG
          1 TTTTTTTG

                    
     156457 TTTTTTTG
          1 TTTTTTTG

               *    
     156465 TTTGTTT-
          1 TTTTTTTG

              **    
     156472 TTGGTTT-
          1 TTTTTTTG

                    
     156479 TTTTTTTG
          1 TTTTTTTG

                   
     156487 TTTTTTT
          1 TTTTTTT

     156494 TGTATGAAGG


Statistics
Matches: 38,  Mismatches: 6, Indels: 2
        0.83            0.13        0.04

Matches are distributed among these distances:
   7   11  0.29
   8   27  0.71

ACGTcount: A:0.00, C:0.00, G:0.15, T:0.85


Consensus pattern (8 bp):   
TTTTTTTG

Done.