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
3444	3'	-55.5	NC_001604.1	+	24161	0.66	0.526979
	Target:  5'- gCAGCAGCCaacucAGCuuccuuucgGGCUuuguUAGCAGCGcGGg -3' miRNA:   3'- aGUCGUCGG-----UCG---------UCGA----AUCGUCGU-CU- -5'
3444	3'	-55.5	NC_001604.1	+	16233	0.66	0.515879
	Target:  5'- -gAGCA-CCAGCAGauu-GCAGUAGGg -3' miRNA:   3'- agUCGUcGGUCGUCgaauCGUCGUCU- -5'
3444	3'	-55.5	NC_001604.1	+	12845	0.67	0.461944
	Target:  5'- aCAGCccaAGCCugagcgcauguaGGcCAGCUUAGCgAGCAGu -3' miRNA:   3'- aGUCG---UCGG------------UC-GUCGAAUCG-UCGUCu -5'
3444	3'	-55.5	NC_001604.1	+	23758	0.68	0.401386
	Target:  5'- cCAGCAccaCCAGCGGUg-AGguGCGGAa -3' miRNA:   3'- aGUCGUc--GGUCGUCGaaUCguCGUCU- -5'
3444	3'	-55.5	NC_001604.1	+	21841	0.69	0.354946
	Target:  5'- aUCAGCGG-CAGCAGCcaUAGCcucAGguGAa -3' miRNA:   3'- -AGUCGUCgGUCGUCGa-AUCG---UCguCU- -5'
3444	3'	-55.5	NC_001604.1	+	12171	0.72	0.245864
	Target:  5'- --cGUAGUUGGCAGCgcaugucuucUUAGCGGCAGAg -3' miRNA:   3'- aguCGUCGGUCGUCG----------AAUCGUCGUCU- -5'
3444	3'	-55.5	NC_001604.1	+	5331	1.09	0.000418
	Target:  5'- cUCAGCAGCCAGCAGCUUAGCAGCAGAc -3' miRNA:   3'- -AGUCGUCGGUCGUCGAAUCGUCGUCU- -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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