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
30473	5'	-54.5	NC_006548.1	+	9350	0.66	0.638597
	Target:  5'- cUGGCAGGGgUGCUgCGGcaugUUGCCGAGc -3' miRNA:   3'- cACUGUCUCgGUGA-GCC----AACGGCUUc -5'
30473	5'	-54.5	NC_006548.1	+	20073	0.66	0.650016
	Target:  5'- -cGGCAugcucuaugccGAGCCGCaccaGGUggUGCCGGAGu -3' miRNA:   3'- caCUGU-----------CUCGGUGag--CCA--ACGGCUUC- -5'
30473	5'	-54.5	NC_006548.1	+	31278	1.08	0.000882
	Target:  5'- uGUGACAGAGCCACUCGGUUGCCGAAGc -3' miRNA:   3'- -CACUGUCUCGGUGAGCCAACGGCUUC- -5'
30473	5'	-54.5	NC_006548.1	+	31146	0.77	0.146033
	Target:  5'- cUGAUugcguAGAGCCACg-GGUUGCCGGAGc -3' miRNA:   3'- cACUG-----UCUCGGUGagCCAACGGCUUC- -5'
30473	5'	-54.5	NC_006548.1	+	7174	0.68	0.493203
	Target:  5'- -gGGCAGAGCCGCcUGGggcgUGaCGAGGc -3' miRNA:   3'- caCUGUCUCGGUGaGCCa---ACgGCUUC- -5'
30473	5'	-54.5	NC_006548.1	+	34733	0.68	0.503954
	Target:  5'- aGUGGcCGGuGCCGucCUCGGUcUGCgGAAGa -3' miRNA:   3'- -CACU-GUCuCGGU--GAGCCA-ACGgCUUC- -5'
30473	5'	-54.5	NC_006548.1	+	31733	0.66	0.650016
	Target:  5'- -cGaACGGcAGCCACUCGGgcgagggGCCGc-- -3' miRNA:   3'- caC-UGUC-UCGGUGAGCCaa-----CGGCuuc -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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