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
8179	5'	-51.6	NC_001978.2	+	35063	0.66	0.830849
	Target:  5'- gGACagAUCgAACGGcacUGAGUGCGGCa -3' miRNA:   3'- -CUGg-UAG-UUGCCagaACUCAUGCCGa -5'
8179	5'	-51.6	NC_001978.2	+	5446	0.66	0.82128
	Target:  5'- -uCCAUgGGCGG-CUUcaAGUACGGCUu -3' miRNA:   3'- cuGGUAgUUGCCaGAAc-UCAUGCCGA- -5'
8179	5'	-51.6	NC_001978.2	+	17723	0.67	0.759677
	Target:  5'- aGACCGUUGAUGGUCaccUUGuaccGGgcgACGGCUc -3' miRNA:   3'- -CUGGUAGUUGCCAG---AAC----UCa--UGCCGA- -5'
8179	5'	-51.6	NC_001978.2	+	2561	0.67	0.748829
	Target:  5'- uGCCGU-GACGGUCgacUGAGccacgACGGCa -3' miRNA:   3'- cUGGUAgUUGCCAGa--ACUCa----UGCCGa -5'
8179	5'	-51.6	NC_001978.2	+	17803	0.68	0.703125
	Target:  5'- cGACCAacuaugccgcguuUCAGCGGUCgUUGGGcUAcucCGGCa -3' miRNA:   3'- -CUGGU-------------AGUUGCCAG-AACUC-AU---GCCGa -5'
8179	5'	-51.6	NC_001978.2	+	10097	0.68	0.676865
	Target:  5'- cGACCAUCAACgccgguaaggcaguGGUCgccUGGGUgacgucaagcgcgACGGCg -3' miRNA:   3'- -CUGGUAGUUG--------------CCAGa--ACUCA-------------UGCCGa -5'
8179	5'	-51.6	NC_001978.2	+	17668	1.08	0.001753
	Target:  5'- uGACCAUCAACGGUCUUGAGUACGGCUa -3' miRNA:   3'- -CUGGUAGUUGCCAGAACUCAUGCCGA- -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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