blat - Standalone BLAT v. 9 fast sequence search command line tool
usage:
   blat database query [-ooc=11.ooc] output.psl
where:
   database is either a .fa file, a .nib file, or a list of .fa or .nib files
   query is similarly a .fa, .nib, or list of .fa or .nib files
   -ooc=11.ooc tells the program to load over-occurring 11-mers from
               and external file.  This will increase the speed
               by a factor of 40 in many cases, but is not required
   output.psl is where to put the output.
options:
   -tileSize=N sets the size of match that triggers an alignment.  
               Usually between 8 and 12
               Default is 11 for DNA and 5 for protein.
   -oneOff=N   If set to 1 this allows one mismatch in tile and still
               triggers an alignments.  Default is 0.
   -minMatch=N sets the number of tile matches.  Usually set from 2 to 4
               Default is 2 for nucleotide, 1 for protein.
   -minScore=N sets minimum score.  This is twice the matches minus the mismatches
               minus some sort of gap penalty.  Default is 30
   -minIdentity=N Sets minimum sequence identity (in percent).  Default is 90 for
               nucleotide searches, 25 for protein or translated protein searches.
   -maxGap=N   sets the size of maximum gap between tiles in a clump.  Usually set
               from 0 to 3.  Default is 2. Only relevent for minMatch > 1.
   -noHead     suppress .psl header (so it's just a tab-separated file)
   -ooc=N.ooc  Use overused tile file N.ooc.  N should correspond to 
               the tileSize
   -makeOoc=N.ooc Make overused tile file
   -repMatch=N sets the number of repetitions of a tile allowed before
               it is marked as overused.  Typically this is 256 for tileSize 12,
               1024 for tile size 11, 4096 for tile size 10.
               Default is 1024.  Typically only comes into play with makeOoc
   -mask=type  Mask out repeats.  Alignments won't be started in masked region but
               may extend through it.  Masking only works for nucleotides. Mask types are:
                 lower - mask out lower cased sequence
                 upper - mask out upper cased sequence
                 out   - mask according to database.out RepeatMasker .out file
                 file.out - mask database according to RepeatMasker file.out
   -qMask=type Mask out repeats in query sequence.  Alignments won't be started in masked
               region but may extend through it.  Masking only works for nucleotides. Mask:
               types are:
                 lower - mask out lower cased sequence
                 upper - mask out upper cased sequence
   -minRepDivergence=NN - minimum percent divergence of repeats to allow them to be
               unmasked.  Default is 15
   -out=type   Controls output file format.  Type is one of:
                   psl - Default.  Tab separated format without actual sequence
                   pslx - Tab separated format with sequence
   -dots=N     Output dot every N sequences to show program's progress
   -t=type     Database type.  Type is one of:
                 dna - DNA sequence
                 prot - protein sequence
                 dnax - DNA sequence translated in six frames to protein
               The default is dna
   -q=type     Query type.  Type is one of:
                 dna - DNA sequence
                 rna - RNA sequence
                 prot - protein sequence
                 dnax - DNA sequence translated in six frames to protein
                 rnax - DNA sequence translated in three frames to protein
               The default is dna
   -prot       Synonymous with -d=prot -q=prot