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
7333	3'	-54.8	NC_001900.1	+	45228	0.66	0.759911
	Target:  5'- uGGUCgaGCGUCaCGGGugGcUGGAagcaUGGAa -3' miRNA:   3'- -CCAG--UGUAGgGCUCugC-ACCUg---ACCU- -5'
7333	3'	-54.8	NC_001900.1	+	32666	0.66	0.748563
	Target:  5'- --cCACAUCCUc-GACGUGGgccaugagucgguGCUGGAg -3' miRNA:   3'- ccaGUGUAGGGcuCUGCACC-------------UGACCU- -5'
7333	3'	-54.8	NC_001900.1	+	43322	0.67	0.696485
	Target:  5'- aGGUaGCGgaggaCCGAGAC-UGGGCUGGc -3' miRNA:   3'- -CCAgUGUag---GGCUCUGcACCUGACCu -5'
7333	3'	-54.8	NC_001900.1	+	5083	0.67	0.696485
	Target:  5'- aGGUCucGCAa--CGAGGCGUcGACUGGGa -3' miRNA:   3'- -CCAG--UGUaggGCUCUGCAcCUGACCU- -5'
7333	3'	-54.8	NC_001900.1	+	15085	0.67	0.663777
	Target:  5'- uGUC-CGaCCCGucGACcUGGACUGGAg -3' miRNA:   3'- cCAGuGUaGGGCu-CUGcACCUGACCU- -5'
7333	3'	-54.8	NC_001900.1	+	19989	0.7	0.500331
	Target:  5'- uGGUUACccuucggcUCCCGAGGcCGUGGucgcgcuGCUGGGg -3' miRNA:   3'- -CCAGUGu-------AGGGCUCU-GCACC-------UGACCU- -5'
7333	3'	-54.8	NC_001900.1	+	29528	1.11	0.000806
	Target:  5'- aGGUCACAUCCCGAGACGUGGACUGGAu -3' miRNA:   3'- -CCAGUGUAGGGCUCUGCACCUGACCU- -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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