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
30599	5'	-56.1	NC_006549.1	+	31386	0.66	0.881729
	Target:  5'- cGGGuu-CGUCGCGCCaGuCuCCGCGGu -3' miRNA:   3'- -CCCuuuGCAGCGCGGaCuGcGGUGUU- -5'
30599	5'	-56.1	NC_006549.1	+	92382	0.66	0.872345
	Target:  5'- uGGGAAaccaaaaaaagauuACGUC-CGaCCUGACGCaCGCc- -3' miRNA:   3'- -CCCUU--------------UGCAGcGC-GGACUGCG-GUGuu -5'
30599	5'	-56.1	NC_006549.1	+	33615	0.68	0.791658
	Target:  5'- uGGGAGGCGuuUCGCGCguagcguauuCUaGCGCCACc- -3' miRNA:   3'- -CCCUUUGC--AGCGCG----------GAcUGCGGUGuu -5'
30599	5'	-56.1	NC_006549.1	+	29299	0.71	0.643118
	Target:  5'- cGGGAAgGCGgucaaaaGCGCC-GugGCCACGGg -3' miRNA:   3'- -CCCUU-UGCag-----CGCGGaCugCGGUGUU- -5'
30599	5'	-56.1	NC_006549.1	+	85877	0.73	0.511206
	Target:  5'- -cGGAGCGUCGUGCUUGuagaacGCGCCACu- -3' miRNA:   3'- ccCUUUGCAGCGCGGAC------UGCGGUGuu -5'
30599	5'	-56.1	NC_006549.1	+	18711	0.8	0.213388
	Target:  5'- uGGGAGACGagacCGCGCUUGACGCCGu-- -3' miRNA:   3'- -CCCUUUGCa---GCGCGGACUGCGGUguu -5'
30599	5'	-56.1	NC_006549.1	+	57027	1.08	0.002865
	Target:  5'- uGGGAAACGUCGCGCCUGACGCCACAAg -3' miRNA:   3'- -CCCUUUGCAGCGCGGACUGCGGUGUU- -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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