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
30602	5'	-54.7	NC_006549.1	+	92226	0.66	0.921256
	Target:  5'- -gGaCGCGCCcGAcGAAGccGAGCUgugCUGCg -3' miRNA:   3'- gaC-GCGCGGcCU-CUUC--UUCGAa--GACG- -5'
30602	5'	-54.7	NC_006549.1	+	130624	0.66	0.914863
	Target:  5'- aUGCGCcaugguGUCGGAacgucugGAAGGAGUggcgCUGCa -3' miRNA:   3'- gACGCG------CGGCCU-------CUUCUUCGaa--GACG- -5'
30602	5'	-54.7	NC_006549.1	+	53313	0.67	0.903118
	Target:  5'- -gGCGCGCaCGGcagacccGAAGAGGCcgCgGCg -3' miRNA:   3'- gaCGCGCG-GCCu------CUUCUUCGaaGaCG- -5'
30602	5'	-54.7	NC_006549.1	+	100748	0.67	0.8828
	Target:  5'- aUGC-CGaguaCGGAgGAGGAGGCUcUCUGUa -3' miRNA:   3'- gACGcGCg---GCCU-CUUCUUCGA-AGACG- -5'
30602	5'	-54.7	NC_006549.1	+	5192	0.67	0.875559
	Target:  5'- gUGCGUGCauuGGGGAGGAacguGGCacaccaCUGCa -3' miRNA:   3'- gACGCGCGg--CCUCUUCU----UCGaa----GACG- -5'
30602	5'	-54.7	NC_006549.1	+	5293	0.69	0.818898
	Target:  5'- -gGCGCGCUGGuGuGGggGUUaUCaUGCa -3' miRNA:   3'- gaCGCGCGGCCuCuUCuuCGA-AG-ACG- -5'
30602	5'	-54.7	NC_006549.1	+	72013	1.12	0.001889
	Target:  5'- gCUGCGCGCCGGAGAAGAAGCUUCUGCg -3' miRNA:   3'- -GACGCGCGGCCUCUUCUUCGAAGACG- -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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