I have a problem with bowtie alignment, I used bowtie to find match sequence in fastq file with rfam sequence list. I tested it in 2 different conditions: with and without miRNAs sequence in rfam list. But there is a big difference between result in these 2 different condition. When I used complete list of rfam as index , number of match sequence to piRNA is 3,710,548 but after removing miRNAs from rfam list , match seq to piRNA is about 820,000 why I have a big difference in these 2 condition , size of index has influence on alignment ?

Bowtile lunched with this command :

 bowtie /bowtie_index/with-withoutmiRNA_Rfam  in.fq -v 1 --best out.fq

Thanks