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
18955	5'	-53.6	NC_004683.1	+	42586	0.66	0.819143
	Target:  5'- cGCG-GCGGUCgGGgcCGGUCGUccGGCUg -3' miRNA:   3'- -CGUaCGCCAGgCUa-GCUAGUA--CCGAg -5'
18955	5'	-53.6	NC_004683.1	+	21274	0.66	0.800063
	Target:  5'- aGCAgGCGGgg-GAUCGA-CAUGGCa- -3' miRNA:   3'- -CGUaCGCCaggCUAGCUaGUACCGag -5'
18955	5'	-53.6	NC_004683.1	+	28878	0.66	0.787272
	Target:  5'- ---cGCGGUCaCGAUCGAUCcgccauguucgcgaAUGGaCUg -3' miRNA:   3'- cguaCGCCAG-GCUAGCUAG--------------UACC-GAg -5'
18955	5'	-53.6	NC_004683.1	+	15333	0.67	0.75881
	Target:  5'- aGCA-GCGGcCCGAacUCGAUCAUcuccgucgacccgGGCg- -3' miRNA:   3'- -CGUaCGCCaGGCU--AGCUAGUA-------------CCGag -5'
18955	5'	-53.6	NC_004683.1	+	2703	0.68	0.706663
	Target:  5'- cGgAUGCGGcCCGAUUGGgucgaCGUGGUggUCg -3' miRNA:   3'- -CgUACGCCaGGCUAGCUa----GUACCG--AG- -5'
18955	5'	-53.6	NC_004683.1	+	43134	0.71	0.519884
	Target:  5'- gGCGUGCGGcugcguggCCgGAUCGA-C-UGGCUCa -3' miRNA:   3'- -CGUACGCCa-------GG-CUAGCUaGuACCGAG- -5'
18955	5'	-53.6	NC_004683.1	+	49841	1.12	0.000895
	Target:  5'- gGCAUGCGGUCCGAUCGAUCAUGGCUCg -3' miRNA:   3'- -CGUACGCCAGGCUAGCUAGUACCGAG- -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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