Figure 1

General Display Features. Line 1: Mismatch frequency plot. 2: Read coverage histogram. 3: Structure of the region (mirtron between two exons). 4: Reference sequence. 5: Reads & Libraries (library list in the menu in the center, selected library highlighted in pink). Identical reads are summarized as a bar with the number of reads. Colors on top of the bar show mismatches (compared to the reference genome sequence). 6: Read sequences are shown (with the similar color of mismatches). 7: Secondary structure with reference sequence from mirBase. The bottom line shows single-stranded regions in magenta. The double-stranded regions in blue are above, with base pairing encoded (if a user clicks on a position in this line, its corresponding base-pair in a stem will be connected by a magenta line in the display, as shown). Green boxes show bulge lengths in the RNA strand opposite to the bulge.