This allowed a maximum of one mismatch within a 20 nt seed region and a maximum of two mismatches across the entire alignment.
Although quality scores could be applied in the validation step of our algorithm, it remains unclear to us how best to make tradeoffs between quality scores and alignment results, for example, how to choose between an alignment with one mismatch at a high-quality score or one with two mismatches at lower quality scores.
And chances are, that teammate creates a one-on-one mismatch because, as an offensive player facing a defender, he has the advantage of knowing where the next step is going.
If BWA was unable to align any of the probe sequences in a given probe-set with a maximum of one mismatch, that probe-set was annotated as unaligned.
For the selection of the computing algorithm, we chose a tolerance of one mismatch for mapping, which resulted in a total of 16,461,503 reads (86.32%) that represent 26,984 unique sRNAs were mapped to the reference genome (Additional file 2: Figure S1).
No significant over-representation of the 9 bp motif downstream of microRNA loci was detected as compared with coding genes (the P-value of a two-tailed G-test for patterns with a maximum of one mismatch was p = 0.066).
Bioinformatic analysis of the binding sites showed that only 13% contained a full consensus CRE element, the majority contained either a CRE with one mismatch or one or several half-CRE elements (Fig. 1A).
Separate databases were created for perfect repeats, arrays with a maximum of one mismatch allowed per ten bp of repeat sequence, and arrays with a maximum of one mismatch per six bp.
Core promoters with a minimal canonical TATA box (TATA), a TATA-box with one mismatch (TATA-1), a TATA-box with two mismatches (TATA-2) and the remainder of the genes (TATA-less) comprised the four gene groups.
The positions of SSR markers were determined on the basis of the alignment between the primers and the genomic sequence of Nipponbare; a maximum of one mismatch or indel was allowed in e-PCR.
