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Table 29 Top entropy hits of E. coli filtered for GC- and uracil-comp

From: Secondary structural entropy in RNA switch (Riboswitch) identification

E. coli Start End Strand Upstream operon Dist. to upstream MFE MFE p. Val. GC RND RND p. Val. Uracil Dist. to downstream Downstream operon Probability
100 nt 4083889 4083988 forward yiiF -5848 -38.4 0.0267 0.53 58.6367989 0.0365 0.29 102 fdhD 0.789
100 nt 187962 188061 forward cdaR -4293 -36.4 0.0466 0.53 59.0985985 0.0229 0.32 1702 rpsB,tff,tsf 0.776
100 nt 952485 952584 forward ycaK -2955 -36.8 0.0419 0.52 58.3203011 0.0494 0.27 3452 ycaP 0.765
100 nt 4115038 4115137 forward uspD,yiiS -3245 -37 0.0396 0.53 58.3563995 0.0477 0.33 1452 zapB 0.756
E. coli Start End Strand Upstream operon Dist. to upstream MFE MFE p. Val. GC RND RND p. Val. Uracil Dist. to downstream Downstream operon Probability
150 nt 2686923 2687072 forward hmp -1802 -56.00 - 0.5333 90.7522964 0.0077 0.32000 6827 mltF 0.8671584129
150 nt 2887386 2887535 forward iap -11672 -56.40 - 0.5333 89.1240005 - 0.0294 2777 queD 0.8254097700
150 nt 3467187 3467336 forward gspO1 -2871 -56.10 - 0.5200 88.5419006 0.0450 0.29333 8402 slyX 0.8172816634
150 nt 3576825 3576974 reverse yhhW -74 -55.60 - 0.4800 88.6371994 0.0419 0.30666 149 gntK,gntR,gntU 0.8547886610
150 nt 2195866 2196015 reverse yehS -13808 -58.00 - 0.5333 88.6897964 0.0405 0.27333 3749 mrp 0.8320623040
  1. Significant hits of the forward and reverse strands of the E. coli intergenic regions having significantly high RND entropy (p-Val. <0.0500), significantly low (p.Val. <0.050), GC and uracil compositions within the range of those for known riboswitches Threshold values and their corresponding p-values have been calculated separately for each genome-wide test. 50 nt overlap used for 100 nt scan (100090 segments). 175 nt overlap used for 150 nt scan (66414 segments). Distance from Upstream and Downstream operons are the distance from the center of the hit to the stop and start codons of upstream and downstream operons, respectively. Probability denotes the multinomial regression likelihood of being a riboswitch under the LMFEGCRND model. Positions are according to gbU00096.2 version of E. coli and not gbU00096.3 version. Negative values indicate distance to upstream operon. Columns Upsream/Downstream Operon show gene ID within the operon.
  2. 1Table 29: Complete list of genes in this operon is gspC,gspD,gspE,gspF,gspG,gspH,gspI,gspJ,gspK,gspL,gspM,gspO.