miRNA display CGI

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ID	Location	Perfect MFE.*	RefSeq Acc.	strand	Start Position	R_P_ratio#	P value
	Predicted miRNA align pattern
20577	3'	-52.6	NC_004688.1	+	47703	0.67	0.923227
	Target:  5'- -gCGGGGCGUagcggucuuUGuGAu-AGGCGAGAu -3' miRNA:   3'- cgGCUCCGCA---------ACuCUuuUCCGCUCUu -5'
20577	3'	-52.6	NC_004688.1	+	67785	0.67	0.904693
	Target:  5'- gGCCGuGGGCc---AGAGAAGGCGAGc- -3' miRNA:   3'- -CGGC-UCCGcaacUCUUUUCCGCUCuu -5'
20577	3'	-52.6	NC_004688.1	+	87694	0.68	0.883822
	Target:  5'- cGCCGccugcuGGGCGgccgGAGAGAGGGauugGAGGg -3' miRNA:   3'- -CGGC------UCCGCaa--CUCUUUUCCg---CUCUu -5'
20577	3'	-52.6	NC_004688.1	+	49651	0.68	0.876363
	Target:  5'- gGgCGGGGCGUcgcgguggaucUGGuGGAucGGCGAGGAg -3' miRNA:   3'- -CgGCUCCGCA-----------ACU-CUUuuCCGCUCUU- -5'
20577	3'	-52.6	NC_004688.1	+	71091	0.68	0.868661
	Target:  5'- uGCgGGGGUGagGAGugcGAGGGUGAGGg -3' miRNA:   3'- -CGgCUCCGCaaCUCu--UUUCCGCUCUu -5'
20577	3'	-52.6	NC_004688.1	+	36990	0.71	0.738765
	Target:  5'- aGCCccccgagGGGGCGUUGAGGucGGG-GAGGAu -3' miRNA:   3'- -CGG-------CUCCGCAACUCUuuUCCgCUCUU- -5'
20577	3'	-52.6	NC_004688.1	+	98411	0.79	0.317064
	Target:  5'- uGCCGAGcGuCGUUGGGAGAuuuGGGUGAGAc -3' miRNA:   3'- -CGGCUC-C-GCAACUCUUU---UCCGCUCUu -5'

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Note:
      When operating RNAhybrid, the pipeline first calculates the perfect minimum free energy (Perfect mfe *) of a putative miRNA when the entire putative miRNA binds to a perfectly complementary target site, then it calculates the minimum free energy of RNA duplex (mfe of the miRNA/mRNA duplex), abbreviated as Rd_mfe. An alignment for which the Rd_mfe to its correspondent Perfect mfe ratio (R_P_ratio #) is more than 66% is regarded as a positive alignment as described by Krek et al. (21). The P_value is calculated by RNAhybrid.

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