Figure 1

A plot showing the ratio of +/+ orientation promoterwise alignments (being collinear with the direction of transcription) versus all alignments for human/mouse (blue lines) and human/chicken (magenta) promoters. The x-axis is the bit score range, binned in 1 bit intervals. The y-axis is the ratio of +/+ alignments to the total number in this range. All species except mouse/rat show similar 'step' behavior between 20 and 25 bits. The depression below 0.5 of mouse/human alignments at low bit scores at first seems surprising, as one expects random data to show a 0.5 ratio. This depression is because there is a significant amount of +/+ alignments which, when close to random alignments, will often capture low scoring alignments, especially if it is straddled by two high scoring alignments, and merge into one high scoring alignment. As this predominantly occurs in forward/forward alignments, this means that there is a depression of low scoring forward/forward alignments.