I/O options:
  database file   : 512_simSeq1_25e-3.fa
  query file      : 512_simSeq2_25e-3.fa
  alphabet        : dna5
  output file     : 25e-3.gff
  output format   : gff

User specified parameters:
  minimal match length             : 50
  maximal error rate (epsilon)     : 0.025
  maximal x-drop                   : 10
  k-mer (q-gram) length            : 7
  search forward strand            : yes
  search reverse complement        : no

  verification strategy            : exact
  maximal number of matches        : 5000
  duplicate removal every          : 10000

Calculated parameters:
  s^min        : 25
  threshold    : 37
  distance cut : 57
  delta        : 16
  overlap      : 2

Loaded 1 query sequence.
Loaded 1 database sequence.

All matches matches resulting from your search have an E-value of: 
        1.74324e-13 or smaller  (match score = 1, error penalty = -2)

Constructing index...

Aligning all query sequences to database sequence...
  seq1 length=1000000 numMatches=500 errorRate=0.025 matchMinLength=50 matchMaxLength=200
    # SWIFT hits      : 582
    Longest hit       : 243
    Avg hit length    : 121

# Eps-matches     : 500
Longest eps-match : 207
Avg match length  : 125
