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
6267	5'	-53.7	NC_001844.1	+	3756	0.66	0.955184
	Target:  5'- ---aGGCGCgccUCCAUGCCUUUUuUAUa -3' miRNA:   3'- acuaCCGCG---AGGUGCGGAAAGcAUGg -5'
6267	5'	-53.7	NC_001844.1	+	96871	0.66	0.951133
	Target:  5'- aGAUGGguugcggGCUCCAUGCCUUagaaGUucuCCa -3' miRNA:   3'- aCUACCg------CGAGGUGCGGAAag--CAu--GG- -5'
6267	5'	-53.7	NC_001844.1	+	93170	0.68	0.890509
	Target:  5'- uUGGUGGCuaGCUCUACGCUggcagUgGcUACCc -3' miRNA:   3'- -ACUACCG--CGAGGUGCGGaa---AgC-AUGG- -5'
6267	5'	-53.7	NC_001844.1	+	82430	0.69	0.883546
	Target:  5'- aUGAUGGCGUUUacaaaucCGUCUUggGUACCc -3' miRNA:   3'- -ACUACCGCGAGgu-----GCGGAAagCAUGG- -5'
6267	5'	-53.7	NC_001844.1	+	144209	0.69	0.879257
	Target:  5'- aGGUGGCGCUCCcggggccagcgaacgGCGCagg-CG-ACCc -3' miRNA:   3'- aCUACCGCGAGG---------------UGCGgaaaGCaUGG- -5'
6267	5'	-53.7	NC_001844.1	+	114315	0.7	0.845388
	Target:  5'- gUGGUGGUGCUCUACuCCc--CGcUACCg -3' miRNA:   3'- -ACUACCGCGAGGUGcGGaaaGC-AUGG- -5'
6267	5'	-53.7	NC_001844.1	+	114490	0.7	0.802254
	Target:  5'- cGAggccUGGCGCcCCGCGCUUaccUUCG-ACCc -3' miRNA:   3'- aCU----ACCGCGaGGUGCGGA---AAGCaUGG- -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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