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
18144	3'	-53.7	NC_004680.1	+	58742	0.66	0.840316
	Target:  5'- --cGGGuuGGGGAGcCGcggucgccggauACGAUGACGu -3' miRNA:   3'- ucaCCCugUCCCUCaGC------------UGUUACUGC- -5'
18144	3'	-53.7	NC_004680.1	+	48368	0.66	0.813042
	Target:  5'- -uUGGGguuccACGaGGAGUCG-CGGUGACGa -3' miRNA:   3'- ucACCC-----UGUcCCUCAGCuGUUACUGC- -5'
18144	3'	-53.7	NC_004680.1	+	58384	0.67	0.793891
	Target:  5'- cAGUGGG-CuGuGGuGUCGGCGGcuuUGGCGa -3' miRNA:   3'- -UCACCCuGuC-CCuCAGCUGUU---ACUGC- -5'
18144	3'	-53.7	NC_004680.1	+	29897	0.67	0.757773
	Target:  5'- uGGUGGGGCAGGGgagaccugaagaaccGGUaCGugcaguacgaACGGUGACc -3' miRNA:   3'- -UCACCCUGUCCC---------------UCA-GC----------UGUUACUGc -5'
18144	3'	-53.7	NC_004680.1	+	51350	0.71	0.54748
	Target:  5'- uGGUGGGuCAGGG-GUgGGCGgaAUGGCu -3' miRNA:   3'- -UCACCCuGUCCCuCAgCUGU--UACUGc -5'
18144	3'	-53.7	NC_004680.1	+	1816	0.74	0.370243
	Target:  5'- cGUGGGGCuGGGAuUCGACGAUcgccgcgugGGCGg -3' miRNA:   3'- uCACCCUGuCCCUcAGCUGUUA---------CUGC- -5'
18144	3'	-53.7	NC_004680.1	+	44525	0.99	0.008825
	Target:  5'- uAGUGGGACAGGGAGUCGACAAUG-CGc -3' miRNA:   3'- -UCACCCUGUCCCUCAGCUGUUACuGC- -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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