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
18664	3'	-55.6	NC_004682.1	+	30166	0.66	0.70468
	Target:  5'- gGUGuuGAucGGUaCCGACCCcgaGGUCGg -3' miRNA:   3'- gUACuuCUucCCA-GGCUGGG---CCAGCa -5'
18664	3'	-55.6	NC_004682.1	+	35600	0.66	0.683042
	Target:  5'- aCGUGAAcucGAAGuGGUCCGAgggcuuCUCGGUCc- -3' miRNA:   3'- -GUACUU---CUUC-CCAGGCU------GGGCCAGca -5'
18664	3'	-55.6	NC_004682.1	+	16334	0.66	0.66121
	Target:  5'- gCAUGAAGGacuGGGG-CCGcGCCCucaacgacGGUCGa -3' miRNA:   3'- -GUACUUCU---UCCCaGGC-UGGG--------CCAGCa -5'
18664	3'	-55.6	NC_004682.1	+	36014	0.67	0.650249
	Target:  5'- uCAUGcGGGAAGaGGUCCGggacgaucugcGCCCGGUa-- -3' miRNA:   3'- -GUAC-UUCUUC-CCAGGC-----------UGGGCCAgca -5'
18664	3'	-55.6	NC_004682.1	+	12669	0.69	0.509613
	Target:  5'- --gGAGGGucacuccucuucGGGGUCCgugcccgcGACCUGGUCGg -3' miRNA:   3'- guaCUUCU------------UCCCAGG--------CUGGGCCAGCa -5'
18664	3'	-55.6	NC_004682.1	+	35409	0.69	0.488931
	Target:  5'- gAUGAcGAAGGcaCCGGCCCaGUCGg -3' miRNA:   3'- gUACUuCUUCCcaGGCUGGGcCAGCa -5'
18664	3'	-55.6	NC_004682.1	+	5732	1.06	0.001472
	Target:  5'- uCAUGAAGAAGGGUCCGACCCGGUCGUu -3' miRNA:   3'- -GUACUUCUUCCCAGGCUGGGCCAGCA- -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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