Diagram representing the subroutine to solve collisions:

<p><b>TN</b> mean trailing RNAP in normal elongation. <b>LN</b> means leading RNAP in normal elongation. <b>LBb</b> means leading RNAP in backtracking backwards movement. <b>LBf</b> means leading RNAP in backtracking forwards movement. <b>TBb</b> means trailing RNAP in backtracking backwards movement. <b>TBf</b> means trailing RNAP in backtracking forwards movement.</p

RNAP position in function of reaction time during a simulation of the <i>MRA</i>:

<p>We can see the kinetic behavior of the RNAP during the <i>MRA</i> for sequence D167: the evolution in time of the position of the enzyme in the DNA strand. Each region represents the space occupied by the enzyme during transcription, and the colors indicate the binding order to the DNA strand. Note that there is no overlap between the regions. Points where the regions touch each other indicate the occurrence of a collision between the molecules. The colored regions represent the space occupied by the enzymes during the reaction. Sites where molecules take longer dwell time to continue transcription and backtracking sites are easy to identify. The collisions between the molecules usually occur at the pause candidate sites.</p

Required time for complete elongation for all RNAPs by the maximum number of RNAP allowed on the template:

<p>Distribution of the 4800 required times to complete transcription of the template by the maximum number of RNAP allowed. The upper and lower limits of each bar indicates respectively the first and third quartiles of these distributions, with a median highlighted in white. The colors represent the RNAP binding order.</p

Relative transcription efficiency,

<p><b>:</b> Each color represents a sequence, as indicated at the end of the respective curve. The values are shown as a function of the maximum number of enzymes allowed during the simulation. Note that the asymptotic values of curves are sequence dependent.</p

Representation of time evolution of RNAP:

<p>The red lines represent the last simulated step. a) The time evolution for a single molecule. We consider that the movement is uniform between each step. The velocity is assigned by the Gillespie algorithm. b) The method used to solve collisions. In blue we show the leader RNAP and in black the trailing RNAP. represents the required time for the collision. is the time for the first event among the following possibilities: nucleotide inclusion by trailing RNAP, nucleotide inclusion by leading RNAP or collision.</p

Parameters Values.

<p>Parameters values for <b>Eq. 3</b>. These NTP-dependent parameters were experimentally determined by Bai <i>et al.</i><a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0057328#pone.0057328-Bai2" target="_blank">[15]</a>.</p

Distribution of the distances covered by backtracked RNAPs from the backtracking site:

<p>The lower and upper limits of the boxes correspond respectively to the first and third quartiles. The median is highlighted in white.</p

Elongation kinetics for sequences D167 and D387:

<p>a) Dwell times between nucleotide incorporation by the RNA strand length. Green: <i>SRA</i>; Blue: <i>MRA</i>. The lines are almost overlapped: differences between them arise only in sites with larger dwell times. b) Forty larger values of dwell time for <i>SRA</i> (upward triangle, green) and the value for the correspondent site in <i>MRA</i> (downward triangle, blue). The graph is on a logarithmic scale.</p

Relation between the incorrect and correct prediction, :

<p>The error bars represent the standard deviation obtained by a bootstrap technique. In this case, we evaluated the impact of the finite number of studied sequences on .</p

Comparison among the simulated transcription gels in different times:

<p>a) Template D167. b) Template D387. Each column represents the reaction time for that simulation. The intensity of the bands is proportional to the amount of produced transcripts of that length in the allowed time. The experimental results shown here are graphical reproductions of the gels presented in the experimental work of Bai and Wang <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0057328#pone.0057328-Bai3" target="_blank">[23]</a>. The experimentally observed bands are indicated with their respective transcript size. Some false positives present in the <i>SRA</i> appear less intense in the <i>MRA</i>. For the single-round and the multi-round elongation: some bands appear earlier in <i>MRA</i> than in <i>SRA</i> and the predicted intensities are different for most bands.</p