PerPlot & PerScan: tools for analysis of DNA curvature-related periodicity in genomic nucleotide sequences

Table 1 MaxQ index percentiles in random sequences^a.

Method^b	MaxQ percentiles for five different spacing ranges^c
	40 bp	70 bp	100 bp	150 bp	200 bp
AT	3.07, 2.57, 1.80^d	3.15, 2.71, 1.99	3.18, 2.79, 2.10	3.26, 2.89, 2.23	3.32, 2.96, 2.31
A2T2	2.98, 2.52, 1.80	3.08, 2.66, 1.98	3.17, 2.77, 2.09	3.26, 2.90, 2.23	3.36, 2.98, 2.32
A3T3	2.89, 2.50, 1.80	3.05, 2.65, 1.99	3.17, 2.77, 2.11	3.28, 2.90, 2.24	3.35, 2.99, 2.33
A4T4	2.90, 2.45, 1.79	3.03, 2.64, 1.99	3.15, 2.76, 2.11	3.27, 2.91, 2.24	3.39, 3.01, 2.34
A5T5	2.81, 2.42, 1.77	2.96, 2.60, 1.96	3.11, 2.73, 2.09	3.21, 2.88, 2.23	3.33, 2.98, 2.33
AT2	2.97, 2.50, 1.79	3.08, 2.66, 1.98	3.16, 2.76, 2.10	3.24, 2.88, 2.23	3.32, 2.96, 2.31
AT3	2.94, 2.48, 1.80	3.07, 2.66, 1.98	3.15, 2.77, 2.11	3.28, 2.90, 2.24	3.37, 3.00, 2.33
AT4	2.88, 2.47, 1.79	3.05, 2.65, 1.99	3.17, 2.77, 2.12	3.27, 2.91, 2.25	3.39, 3.01, 2.35
AT5	2.90, 2.45, 1.79	3.01, 2.62, 1.99	3.14, 2.76, 2.11	3.27, 2.92, 2.26	3.40, 3.02, 2.35
AT6	2.78, 2.40, 1.75	2.96, 2.59, 1.94	3.08, 2.73, 2.07	3.24, 2.88, 2.21	3.35, 2.98, 2.31

^a MaxQ measures the highest periodic signal intensity detected over the range or periods 5-20 bp. The table shows the 99^th, 95^th, and 50^th percentile, for each combination of parameters. See text for details.
^b Definition of A-tracts: "AT", single nucleotides A or T; "A2T2" dinucleotides AA or TT; "AT2", dinucleotides AA, AT, or TT; "A3T3" trinucleotides AAA or TTT; "AT3", trinucleotides AAA, AAT, ATT, or TTT; etc.
^c The spacing range refers to the difference between parameters s_max-s_min. The simulations were performed for spacing range values 40, 70, 100, 150, and 200 bp. See text for details.
^d The 99^th, 95^th, and 50^th percentiles, respectively, of the MaxQ values in 20,500 random sequences are shown.