Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: scaffold_594 ID=scaffold_594-JGI_221_v2.0

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: 6544
ACGTcount: A:0.28, C:0.12, G:0.13, T:0.29

Warning! 1167 characters in sequence are not A, C, G, or T


Found at i:1313 original size:16 final size:15

Alignment explanation


    Indices: 1283--1321  Score: 51
    Period size: 16  Copynumber: 2.5  Consensus size: 15

       1273 TGTTTAGTCA

                      *    
       1283 TTAGGGTTTTTTGGT
          1 TTAGGGTTTTATGGT

                            
       1298 TTAGGGATTTTATGGT
          1 TTAGGG-TTTTATGGT

               *    
       1314 TTAAGGTT
          1 TTAGGGTT

       1322 AGGATTTTGT


Statistics
Matches: 21,  Mismatches: 2, Indels: 2
        0.84            0.08        0.08

Matches are distributed among these distances:
  15    8  0.38
  16   13  0.62

ACGTcount: A:0.15, C:0.00, G:0.31, T:0.54


Consensus pattern (15 bp):   
TTAGGGTTTTATGGT

Found at i:3751 original size:16 final size:17

Alignment explanation


    Indices: 3715--3756  Score: 68
    Period size: 17  Copynumber: 2.5  Consensus size: 17

       3705 TCCAAACTTG

                             
       3715 AAAATAATTTAAAACTA
          1 AAAATAATTTAAAACTA

                            *
       3732 AAAATAATTTAAAA-TT
          1 AAAATAATTTAAAACTA

                     
       3748 AAAATAATT
          1 AAAATAATT

       3757 CAAACCCAAA


Statistics
Matches: 24,  Mismatches: 1, Indels: 1
        0.92            0.04        0.04

Matches are distributed among these distances:
  16   10  0.42
  17   14  0.58

ACGTcount: A:0.64, C:0.02, G:0.00, T:0.33


Consensus pattern (17 bp):   
AAAATAATTTAAAACTA
Done.