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
16982	5'	-56.9	NC_004323.1	+	35471	0.66	0.856463
	Target:  5'- -gGGCGcuuGUUGGugCgGCgGCGgAUCg -3' miRNA:   3'- cgCCGUu--CAACCugGgUGgCGCgUAG- -5'
16982	5'	-56.9	NC_004323.1	+	38700	1.1	0.001628
	Target:  5'- uGCGGCAAGUUGGACCCACCGCGCAUCc -3' miRNA:   3'- -CGCCGUUCAACCUGGGUGGCGCGUAG- -5'
16982	5'	-56.9	NC_004323.1	+	38906	0.71	0.577641
	Target:  5'- gGCGuGCGGGUUGucauauuUCCGCCGCGCAc- -3' miRNA:   3'- -CGC-CGUUCAACcu-----GGGUGGCGCGUag -5'
16982	5'	-56.9	NC_004323.1	+	85813	0.72	0.494029
	Target:  5'- gGCGGCGAGguccgcguuCCCGCCGCGUAc- -3' miRNA:   3'- -CGCCGUUCaaccu----GGGUGGCGCGUag -5'
16982	5'	-56.9	NC_004323.1	+	85970	0.72	0.488254
	Target:  5'- cGCGGCGGGaaacgcGGACCUcgccGCCGCGCcaacGUCc -3' miRNA:   3'- -CGCCGUUCaa----CCUGGG----UGGCGCG----UAG- -5'
16982	5'	-56.9	NC_004323.1	+	107362	0.66	0.84046
	Target:  5'- gGCGGCucaUUGGAuCCCAacaCaCGCGUCg -3' miRNA:   3'- -CGCCGuucAACCU-GGGUg--GcGCGUAG- -5'
16982	5'	-56.9	NC_004323.1	+	126874	0.68	0.758927
	Target:  5'- aGCGGCAAGUUaauGCCCAUCauuuuguugauagGCGCAg- -3' miRNA:   3'- -CGCCGUUCAAcc-UGGGUGG-------------CGCGUag -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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