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
31934	5'	-54.2	NC_006940.1	+	3047	0.66	0.730633
	Target:  5'- aGUcUCAGAUGuGCggGCGUCGCGuuucagcaaACCa -3' miRNA:   3'- -CGuGGUCUAC-CGaaUGCAGCGC---------UGGc -5'
31934	5'	-54.2	NC_006940.1	+	19791	0.66	0.719781
	Target:  5'- cGgACgGGAUaugugGGCUUACGcuugUGCGGCCa -3' miRNA:   3'- -CgUGgUCUA-----CCGAAUGCa---GCGCUGGc -5'
31934	5'	-54.2	NC_006940.1	+	10025	0.67	0.664399
	Target:  5'- aCACC-GAUGGUaaUUAuCGUCaGCGACUGu -3' miRNA:   3'- cGUGGuCUACCG--AAU-GCAG-CGCUGGC- -5'
31934	5'	-54.2	NC_006940.1	+	40293	0.68	0.607096
	Target:  5'- gGUGCCGGAUGGgUauaagauuaagggUACGUCGUcACUGg -3' miRNA:   3'- -CGUGGUCUACCgA-------------AUGCAGCGcUGGC- -5'
31934	5'	-54.2	NC_006940.1	+	19400	0.69	0.519883
	Target:  5'- cGUACCGGAU-GCggaugAUGUCGCcACCGg -3' miRNA:   3'- -CGUGGUCUAcCGaa---UGCAGCGcUGGC- -5'
31934	5'	-54.2	NC_006940.1	+	38865	0.7	0.477568
	Target:  5'- uCACCGGAcUGGCUgcCGUUGUaGCCGc -3' miRNA:   3'- cGUGGUCU-ACCGAauGCAGCGcUGGC- -5'
31934	5'	-54.2	NC_006940.1	+	40338	1.1	0.000778
	Target:  5'- gGCACCAGAUGGCUUACGUCGCGACCGu -3' miRNA:   3'- -CGUGGUCUACCGAAUGCAGCGCUGGC- -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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