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
30753	3'	-56.5	NC_006552.1	+	28800	0.66	0.706586
	Target:  5'- aGCGUCCacugcGACcaGGGUGgCGGGUUCAa -3' miRNA:   3'- cCGCAGG-----CUGuaCCUACgGCCUAGGU- -5'
30753	3'	-56.5	NC_006552.1	+	26444	0.66	0.685494
	Target:  5'- cGGCG-CCGACuccUGGggGCCGcGcagCCAc -3' miRNA:   3'- -CCGCaGGCUGu--ACCuaCGGC-Cua-GGU- -5'
30753	3'	-56.5	NC_006552.1	+	21168	0.68	0.599969
	Target:  5'- aGGCGcaUCCGGCcgcGUcGGUGCCGGcacAUCCGc -3' miRNA:   3'- -CCGC--AGGCUG---UAcCUACGGCC---UAGGU- -5'
30753	3'	-56.5	NC_006552.1	+	22191	0.71	0.417643
	Target:  5'- gGGCGUCauCGACGUgcaggacacgaaGGGUGCCGGugacgcgAUCCGc -3' miRNA:   3'- -CCGCAG--GCUGUA------------CCUACGGCC-------UAGGU- -5'
30753	3'	-56.5	NC_006552.1	+	20954	0.73	0.341084
	Target:  5'- gGGCGUCCGGCAccgGGAuggccgucaUGCuCGGcgcGUCCGg -3' miRNA:   3'- -CCGCAGGCUGUa--CCU---------ACG-GCC---UAGGU- -5'
30753	3'	-56.5	NC_006552.1	+	28235	0.79	0.13967
	Target:  5'- cGGCGUCaCGuuGUGGAUGCgCGGAUCg- -3' miRNA:   3'- -CCGCAG-GCugUACCUACG-GCCUAGgu -5'
30753	3'	-56.5	NC_006552.1	+	35302	1.1	0.000865
	Target:  5'- gGGCGUCCGACAUGGAUGCCGGAUCCAu -3' miRNA:   3'- -CCGCAGGCUGUACCUACGGCCUAGGU- -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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