Fig. 1

Overview of the stratified alignment strategy used to map short Illumina tags to human pre-microRNAs or whole genome. Three steps allowing respectively 0, 1 and 2 mismatches were used. In each step, tags were iteratively trimmed at the 3′ end until hits could be found with respect to the number of allowed mismatches. A tag was mapped at iteration i if i nucleotides were removed at its 3′ end before hits could be found. Trimmed tags that could not be mapped before they reached the minimum length of 18 bp were forwarded to the next step where the number of allowed mismatches was gradually increased. This ensured that tags with mixed 3′ addition and genomic variation, such as t4, will show only the real genomic variation when aligned on human precursors or whole genome