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
28427	3'	-54.5	NC_005946.1	+	44700	0.66	0.852996
	Target:  5'- --gCCCUgguGGCCCu-GACUGcUGCAc -3' miRNA:   3'- gaaGGGAaguCCGGGuuCUGAC-ACGU- -5'
28427	3'	-54.5	NC_005946.1	+	73759	0.66	0.852996
	Target:  5'- -gUCCUggucCAGG-CCAAGACUGacUGCAg -3' miRNA:   3'- gaAGGGaa--GUCCgGGUUCUGAC--ACGU- -5'
28427	3'	-54.5	NC_005946.1	+	74003	0.67	0.844672
	Target:  5'- --aCCC--CAGGCUgGAG-CUGUGCAa -3' miRNA:   3'- gaaGGGaaGUCCGGgUUCuGACACGU- -5'
28427	3'	-54.5	NC_005946.1	+	10340	0.7	0.689054
	Target:  5'- -cUCCCUUCAGGaugaCgGAGGC-GUGCu -3' miRNA:   3'- gaAGGGAAGUCCg---GgUUCUGaCACGu -5'
28427	3'	-54.5	NC_005946.1	+	13023	0.71	0.582214
	Target:  5'- gUUCCCUgcUCAGGUCCAGGAacCUGUa-- -3' miRNA:   3'- gAAGGGA--AGUCCGGGUUCU--GACAcgu -5'
28427	3'	-54.5	NC_005946.1	+	82580	0.83	0.137121
	Target:  5'- --gCCCUUCAGGCCCGAGACcagGCAc -3' miRNA:   3'- gaaGGGAAGUCCGGGUUCUGacaCGU- -5'
28427	3'	-54.5	NC_005946.1	+	82397	1.08	0.002638
	Target:  5'- cCUUCCCUUCAGGCCCGAGACUGUGCAc -3' miRNA:   3'- -GAAGGGAAGUCCGGGUUCUGACACGU- -5'
28427	3'	-54.5	NC_005946.1	+	82490	1.08	0.002417
	Target:  5'- cCUUCCCUUCAGGCCCAAGACUGUGCAc -3' miRNA:   3'- -GAAGGGAAGUCCGGGUUCUGACACGU- -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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