Bowtie not mapping 100% about bowtie HOT 1 CLOSED

IIRC, unlike Bowtie 2, BWA and many other mappers, Bowtie does not soft-clip reads. I.e. a missmatch in the beginning/end counts as such. I assume due to the shortness of the sequence, this one mismatch pushes the alignment score below the (default) threshold.

Guessing by the particular length of your read and the sequence name in your example, you might want to have a look at how miRDeep2 maps sRNA-seq reads to pre-miRNAs using Bowtie. 😉 See here for its default number of accepted mismatches. Probably you'll have to optimize the parameters further for your use case of mapping straight to the mature miRNAs.

from bowtie.