Please Note: I re-posting my question from http://blog.mothur.org/2016/07/07/Customization-for-your-region/
My intention is to understand about this observation. Thank you.
Step 1: Obtain the alignment coordinates with respect to silva.seed_v128.align
Align: 16sv4.fasta vs. silva.seed_v128.align
Outcome: Start = 11895, End = 25318, NBases = 292
Using the start and end coordinate information, we trim silva.seed_v128.align database.
Step 2: Align the input 16sv4.fasta against the newly trimmed silva database
Align: 16sv4.fasta vs. silva_seed_v128_16sV4.align ( -> This is the newly Trimmed silva db )
Outcome: Start = 2, End = 13423, NBases = 291
Why is the resulting alignment with the trimmed silva database 1-base less ( 291 bases instead of 292 bases ) ?