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
19624	3'	-45.8	NC_004686.1	+	47391	0.66	0.996625
	Target:  5'- -aACCAGGccgACGUGUUggccggGGUgacgaagauguauUCCGAUCa -3' miRNA:   3'- ucUGGUCU---UGUACAAa-----CCA-------------AGGUUAG- -5'
19624	3'	-45.8	NC_004686.1	+	26530	0.67	0.992236
	Target:  5'- gGGAuCCGGGgaaccucgACAUGUcgUGGUUCCGc-- -3' miRNA:   3'- -UCU-GGUCU--------UGUACAa-ACCAAGGUuag -5'
19624	3'	-45.8	NC_004686.1	+	30286	0.67	0.987841
	Target:  5'- cGGGCauuccguuGGGCA-GUUUGGUUUCGAUCc -3' miRNA:   3'- -UCUGgu------CUUGUaCAAACCAAGGUUAG- -5'
19624	3'	-45.8	NC_004686.1	+	22877	0.69	0.973868
	Target:  5'- cGACCGGAGCAgacauauucguauccGUaucUUGGgaCCGAUCa -3' miRNA:   3'- uCUGGUCUUGUa--------------CA---AACCaaGGUUAG- -5'
19624	3'	-45.8	NC_004686.1	+	50330	0.69	0.97356
	Target:  5'- cGACCAGAACGgucUGUccgUUGGgggCGAUCa -3' miRNA:   3'- uCUGGUCUUGU---ACA---AACCaagGUUAG- -5'
19624	3'	-45.8	NC_004686.1	+	16485	0.71	0.921654
	Target:  5'- uGGGCCAGGACAUGUUcagggaUGGggUCGu-- -3' miRNA:   3'- -UCUGGUCUUGUACAA------ACCaaGGUuag -5'
19624	3'	-45.8	NC_004686.1	+	12761	1.12	0.005859
	Target:  5'- uAGACCAGAACAUGUUUGGUUCCAAUCg -3' miRNA:   3'- -UCUGGUCUUGUACAAACCAAGGUUAG- -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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