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
11361	5'	-62.6	NC_003084.1	+	34839	0.66	0.506033
	Target:  5'- gUACGUgugUgAGUUGGUCGGugaaaguGGGGUGCUg -3' miRNA:   3'- -GUGCGa--GgUCGACCGGCU-------CCCCACGA- -5'
11361	5'	-62.6	NC_003084.1	+	59382	0.66	0.497434
	Target:  5'- uCGCGCacgUUUAGCgGGCUGAGGuGGUGg- -3' miRNA:   3'- -GUGCG---AGGUCGaCCGGCUCC-CCACga -5'
11361	5'	-62.6	NC_003084.1	+	45844	0.66	0.478566
	Target:  5'- aUACGCUCCuucugcggcuugGGCUGGaCCcGGGGcUGCa -3' miRNA:   3'- -GUGCGAGG------------UCGACC-GGcUCCCcACGa -5'
11361	5'	-62.6	NC_003084.1	+	106042	0.66	0.469265
	Target:  5'- -cCGCUCCAuGgaGGCCaGGuGcGGGUGCUu -3' miRNA:   3'- guGCGAGGU-CgaCCGG-CU-C-CCCACGA- -5'
11361	5'	-62.6	NC_003084.1	+	66392	0.67	0.460057
	Target:  5'- aAUGUg-CAGCUgGGCCucucggagGAGGGGUGCa -3' miRNA:   3'- gUGCGagGUCGA-CCGG--------CUCCCCACGa -5'
11361	5'	-62.6	NC_003084.1	+	85135	0.72	0.230898
	Target:  5'- --aGCUgCAgacGCUcGCCGAGGGGUGCUu -3' miRNA:   3'- gugCGAgGU---CGAcCGGCUCCCCACGA- -5'
11361	5'	-62.6	NC_003084.1	+	10368	1.06	0.00065
	Target:  5'- aCACGCUCCAGCUGGCCGAGGGGUGCUu -3' miRNA:   3'- -GUGCGAGGUCGACCGGCUCCCCACGA- -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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