miRNA: 3'- -UCGA-UAGUUGAG-UCU-CGGU---UUGCGAa -5'
miRNA: 3'- ucgauAGUUGAGuc-UCGGUUUGCGAa -5'
miRNA: 3'- -UCGAUAGUUg-----AGUCUCGGU--UUGCGaa -5'
miRNA: 3'- -UCGAUAGUUGAGUCUCGGUUUGCGAA- -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 | |||||||
| 23527 | 5' | -49.9 | NC_005260.1 | + | 155464 | 0.67 | 0.996688 |
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Target: 5'- cAGCUaAUCAGCUCaAGAuGCUAgaaGAUGCUa -3' miRNA: 3'- -UCGA-UAGUUGAG-UCU-CGGU---UUGCGAa -5' |
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| 23527 | 5' | -49.9 | NC_005260.1 | + | 187510 | 0.67 | 0.994674 |
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Target: 5'- ----cUCAACUCuuuAGCCAAACGCUc -3' miRNA: 3'- ucgauAGUUGAGuc-UCGGUUUGCGAa -5' |
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| 23527 | 5' | -49.9 | NC_005260.1 | + | 102418 | 0.77 | 0.738808 |
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Target: 5'- gAGCUAUUAAacaacaUCAGAGCCAcaAACGCa- -3' miRNA: 3'- -UCGAUAGUUg-----AGUCUCGGU--UUGCGaa -5' |
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| 23527 | 5' | -49.9 | NC_005260.1 | + | 187728 | 1.07 | 0.017798 |
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Target: 5'- gAGCUAUCAACUCAGAGCCAAACGCUUg -3' miRNA: 3'- -UCGAUAGUUGAGUCUCGGUUUGCGAA- -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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