Alignment Question

[esdartez]

I am using bowtie2 to align some reads against a consensus sequence for young L1s and the alignments are used to predict new insertions. The consensus sequence is relatively short (~130 bp). We are having an issue where some reads that align very well to the consensus sequence with tools like CLUSTAL, are not aligning with bowtie2. I've tried various settings to see if I could get these reads to align and was only successful at getting one of them. Is there a way to get bowtie2 to report the score for unaligned reads? How does bowtie2 determine the alignment score threshold for a read to be considered aligned? Is there a way to influence or set that threshold?