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
11894	5'	-57.9	NC_003266.2	+	6494	0.67	0.384577
	Target:  5'- cGCgCGCUCguagggacuaaggggCGUGCcCCaGGGCAugGGg -3' miRNA:   3'- aUG-GCGAG---------------GUACGaGGaCCCGUugCC- -5'
11894	5'	-57.9	NC_003266.2	+	25787	0.68	0.332452
	Target:  5'- cUGCCGCUCCuucuuaccggUCUGGGUggUGGg -3' miRNA:   3'- -AUGGCGAGGuacga-----GGACCCGuuGCC- -5'
11894	5'	-57.9	NC_003266.2	+	23057	0.68	0.329168
	Target:  5'- gGCUGCUgCGgcggcggugguUGUUCCUGaGGCGAgGGg -3' miRNA:   3'- aUGGCGAgGU-----------ACGAGGAC-CCGUUgCC- -5'
11894	5'	-57.9	NC_003266.2	+	3640	0.68	0.329168
	Target:  5'- cUGCCGCcagcgCCGUGCgcggaauggCCaUGGGCGcCGGc -3' miRNA:   3'- -AUGGCGa----GGUACGa--------GG-ACCCGUuGCC- -5'
11894	5'	-57.9	NC_003266.2	+	26430	0.69	0.290137
	Target:  5'- aGCCaaUUCAUGCggguggaguagUCCUGGGCGGCGc -3' miRNA:   3'- aUGGcgAGGUACG-----------AGGACCCGUUGCc -5'
11894	5'	-57.9	NC_003266.2	+	4966	0.69	0.273438
	Target:  5'- -cUCGCUCCAggaGCUCCucucgcUGGGCGgagagcgacuccugGCGGa -3' miRNA:   3'- auGGCGAGGUa--CGAGG------ACCCGU--------------UGCC- -5'
11894	5'	-57.9	NC_003266.2	+	19812	1.09	0.000278
	Target:  5'- cUACCGCUCCAUGCUCCUGGGCAACGGg -3' miRNA:   3'- -AUGGCGAGGUACGAGGACCCGUUGCC- -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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