miRNA: 3'- -UAGCCaCAGuuGUGUGUCCCGUCGag -5'
miRNA: 3'- -UAGCCaCA-GUuGUGUGUCC-CGUCGAG- -5'
miRNA: 3'- uaGCCACAGuuG----UGUGUCC-CGUC-GAG- -5'
miRNA: 3'- -UAGCCACAGUUGUGUGUCCCGUCGAG- -5'
Results 1 - 4 of 4 are showing below:
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| ID | Location | Perfect MFE.* | RefSeq Acc. | strand | Start Position | R_P_ratio# |
P value
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| Predicted miRNA align pattern | |||||||
| 758 | 3' | -55.4 | NC_000852.3 | + | 50053 | 0.66 | 0.974643 |
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Target: 5'- uAUCGG-GUC--CGCAUGGGGCGGUa- -3' miRNA: 3'- -UAGCCaCAGuuGUGUGUCCCGUCGag -5' |
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| 758 | 3' | -55.4 | NC_000852.3 | + | 119335 | 0.67 | 0.952185 |
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Target: 5'- aAUCGGaGUgCAuCACGCAGGuGUAGUUCc -3' miRNA: 3'- -UAGCCaCA-GUuGUGUGUCC-CGUCGAG- -5' |
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| 758 | 3' | -55.4 | NC_000852.3 | + | 273971 | 0.69 | 0.895384 |
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Target: 5'- -cCGGUGUCggUcucgGCACAGGaGCAGgUUCu -3' miRNA: 3'- uaGCCACAGuuG----UGUGUCC-CGUC-GAG- -5' |
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| 758 | 3' | -55.4 | NC_000852.3 | + | 175105 | 1.07 | 0.008287 |
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Target: 5'- gAUCGGUGUCAACACACAGGGCAGCUCc -3' miRNA: 3'- -UAGCCACAGUUGUGUGUCCCGUCGAG- -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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