miRNA: 3'- -CCaauCGGGGC---UCGGGA-GCCCaCGUu -5'
miRNA: 3'- cCaaUC-GGGGCUCG-----GGaGCCCACGUU- -5'
miRNA: 3'- -CCAAUCGGGGCUCGGGAGCC-CaCGUU- -5'
Results 1 - 3 of 3 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 | |||||||
| 27438 | 3' | -60.2 | NC_005869.1 | + | 17043 | 0.67 | 0.261225 |
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Target: 5'- cGGgauGUCCCGcacGGCCCUgCGGG-GCAc -3' miRNA: 3'- -CCaauCGGGGC---UCGGGA-GCCCaCGUu -5' |
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| 27438 | 3' | -60.2 | NC_005869.1 | + | 10734 | 0.68 | 0.23526 |
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Target: 5'- cGgcGGcCCCCGAGCggcacCCaCGGGUGCAGc -3' miRNA: 3'- cCaaUC-GGGGCUCG-----GGaGCCCACGUU- -5' |
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| 27438 | 3' | -60.2 | NC_005869.1 | + | 4894 | 0.93 | 0.00285 |
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Target: 5'- uGGUUAGCCCCGAGCCCUCGGuG-GCAAc -3' miRNA: 3'- -CCAAUCGGGGCUCGGGAGCC-CaCGUU- -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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