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
28380	5'	-57.8	NC_005946.1	+	68302	0.66	0.795226
	Target:  5'- uGGCGuAGGCCCUaaagaugucugCGgcGGUGaCGGGGu -3' miRNA:   3'- -CUGC-UCUGGGA-----------GCuaCCACaGCCCCu -5'
28380	5'	-57.8	NC_005946.1	+	9725	0.66	0.76456
	Target:  5'- gGACuGGGCCCUgGAcaugacggccauccUGuUGUCGGGGGu -3' miRNA:   3'- -CUGcUCUGGGAgCU--------------ACcACAGCCCCU- -5'
28380	5'	-57.8	NC_005946.1	+	42365	0.67	0.72866
	Target:  5'- aACGGGACCCUU--UGGgccGUCGGGc- -3' miRNA:   3'- cUGCUCUGGGAGcuACCa--CAGCCCcu -5'
28380	5'	-57.8	NC_005946.1	+	72137	0.69	0.582161
	Target:  5'- cACGGGGCCCUgcCGGUGGUGgccaucaugacggCGGGaGGc -3' miRNA:   3'- cUGCUCUGGGA--GCUACCACa------------GCCC-CU- -5'
28380	5'	-57.8	NC_005946.1	+	32429	0.74	0.339876
	Target:  5'- gGACuGGGACCCUUGuUGGUGUCGuagcacaucaGGGAc -3' miRNA:   3'- -CUG-CUCUGGGAGCuACCACAGC----------CCCU- -5'
28380	5'	-57.8	NC_005946.1	+	98099	0.82	0.108649
	Target:  5'- aGACGuuGgCCUCGAcGGUGUCGGGGAg -3' miRNA:   3'- -CUGCucUgGGAGCUaCCACAGCCCCU- -5'
28380	5'	-57.8	NC_005946.1	+	43845	1.08	0.001606
	Target:  5'- cGACGAGACCCUCGAUGGUGUCGGGGAc -3' miRNA:   3'- -CUGCUCUGGGAGCUACCACAGCCCCU- -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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