Hi, everyone,

I am using BLAST+ to identify homologous genes. I would like to know the default parameters of BLASTN. When typing `blastn -h` or` blastn -help`, I could not find detailed default values. On blast+_user_manual.pdf downloaded from NCBI, I could not find these default settings. Could you please do me a favor? I am particularly concern about word_size, penalty score settings, repeat filter, etc. THANK YOU very much!
1. **`blastn` (megablast) [for highly similar sequences]**

 - word_size = 10
 - match/mismatch scores = 1, -2
 - gap cost = linear
 - filter = low complexity regions

2. **`blastn -task blastn` [quite similar sequences]**

 - word_size = 11
 - match/mismatch scores = 2, -3
 - gap costs = existence: 5, extension: 2
 - filter = low complexity regions

You can find this information at <a href="http://blast.ncbi.nlm.nih.gov/Blast.cgi?PROGRAM=blastn&PAGE_TYPE=BlastSearch&LINK_LOC=blasthome">NCBI BLAST.</a> If you are running local BLAST with `outfmt` 0 or 1, you will also see the parameters at the end of your output file.