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. Author manuscript; available in PMC: 2014 Dec 14.
Published in final edited form as: Methods Mol Biol. 2014;1196:255–278. doi: 10.1007/978-1-4939-1242-1_16

Table 2.

A representative example illustrating our procedure for estimating relative affinities, using data for Exd-Lab binding from Slattery et al. (2011). Shown are the observed counts of all 12-mers in R2, the corresponding fraction in R2 (obtained by dividing by the total observed count), the expected frequency in the initial pool R0 (obtained using the 5th-order Markov model), the fold-enrichment, the initial estimate of the relative affinity obtained by rescaling the fold-enrichment and taking the square root, and the standard error for the relative affinity estimate.

12-mer Observed
Count
in R2		 Observed
Frequency
in R2 (x10−3)		 Estimated
Frequency
in R0 (x 10−7)		 Fold-
Enrichment
from R0 to R2		 Estimated
Relative
Affinity		 Standard
Error
GTAATCAATCAT 114136 1.6892 0.8735 19338.2 1.0000 0.0042
ATGATTGATTAC 135714 2.0086 1.1675 17203.7 0.9432 0.0036
AATGATTGATTA 145612 2.1551 1.3900 15504.2 0.8954 0.0033
TAATCAATCATT 99927 1.4789 1.0299 14359.6 0.8617 0.0039
GATGATTGATTA 116529 1.7247 1.3581 12699.3 0.8104 0.0034
GTCATCAATCAT 61953 0.9169 0.7348 12479.3 0.8033 0.0046
AATGATTGATGA 81746 1.2099 0.9830 12307.8 0.7978 0.0039
ATGATTGATGAC 67902 1.0050 0.8511 11808.3 0.7814 0.0042
ATGATTGATGAG 77316 1.1443 0.9984 11460.8 0.7698 0.0039
: : : : : : :
TTTTTGATATAT 102 0.0015 3.4059 4.4324 0.0151 0.0021
ATTGATATTTTT 103 0.0015 3.4431 4.4275 0.0151 0.0021
ATTATTTATTAT 103 0.0015 3.5303 4.3181 0.0149 0.0021
GTTTTGTTTGAT 100 0.0015 3.4723 4.2623 0.0148 0.0021
TTTTTGATTGTT 117 0.0017 4.1203 4.2026 0.0147 0.0019
TTTTTTTGATTA 116 0.0017 4.2856 4.0060 0.0144 0.0019
ATTTATTATTTT 121 0.0018 4.5488 3.9369 0.0143 0.0018
TTTGTTTGATTT 113 0.0017 4.2748 3.9123 0.0142 0.0019
TTTTTTGATTTA 103 0.0015 4.2609 3.5777 0.0136 0.0019
TTTGTTTGTTTA 103 0.0015 4.5958 3.3170 0.0131 0.0018