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
140	3'	-59.2	AC_000006.1	+	11242	0.66	0.390151
	Target:  5'- --aGCCCGAGGGUcGCu--GGCUGCu -3' miRNA:   3'- gcaCGGGCUCCCGaUGuucCUGGCGu -5'
140	3'	-59.2	AC_000006.1	+	13475	0.66	0.390151
	Target:  5'- cCGUcGCCCcaguuuGGGCUGCA-GGAUgCGCGa -3' miRNA:   3'- -GCA-CGGGcu----CCCGAUGUuCCUG-GCGU- -5'
140	3'	-59.2	AC_000006.1	+	16240	0.66	0.363478
	Target:  5'- --aGCCCGAGGu---CAAGGugCGCc -3' miRNA:   3'- gcaCGGGCUCCcgauGUUCCugGCGu -5'
140	3'	-59.2	AC_000006.1	+	23717	0.66	0.354872
	Target:  5'- --aGCUCGAGGGUgACcAGGACCa-- -3' miRNA:   3'- gcaCGGGCUCCCGaUGuUCCUGGcgu -5'
140	3'	-59.2	AC_000006.1	+	10897	0.67	0.338095
	Target:  5'- -cUGCgCGAGGGCcu---GGACCGCc -3' miRNA:   3'- gcACGgGCUCCCGauguuCCUGGCGu -5'
140	3'	-59.2	AC_000006.1	+	23205	0.68	0.298712
	Target:  5'- gGUGgCa-AGGGCcuCGGGGACCGCAa -3' miRNA:   3'- gCACgGgcUCCCGauGUUCCUGGCGU- -5'
140	3'	-59.2	AC_000006.1	+	18156	0.82	0.026127
	Target:  5'- cCGUGCCCGAguaGGGUUugAacuGGGACCGCGg -3' miRNA:   3'- -GCACGGGCU---CCCGAugU---UCCUGGCGU- -5'
140	3'	-59.2	AC_000006.1	+	20083	1.08	0.000239
	Target:  5'- aCGUGCCCGAGGGCUACAAGGACCGCAu -3' miRNA:   3'- -GCACGGGCUCCCGAUGUUCCUGGCGU- -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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