miRNA: 3'- -CCCuGC-AGAGG--AUCGCAGCUCG-------------GUCU- -5'
miRNA: 3'- ccCUGCAgaGGAUCGCAGCuCGGUCU- -5'
miRNA: 3'- cCCUGCAGA----GGA----UCGCAGCUcGGUCu -5'
miRNA: 3'- cccuGCAGA-GGAUCGCAGCUCGGu--CU- -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 | |||||||
| 28505 | 5' | -56.5 | NC_005946.1 | + | 6291 | 0.68 | 0.72645 |
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Target: 5'- uGGGcUGcUCUCCccUGGCGUCGAGCaccuuuguguacuCAGAg -3' miRNA: 3'- -CCCuGC-AGAGG--AUCGCAGCUCG-------------GUCU- -5' |
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| 28505 | 5' | -56.5 | NC_005946.1 | + | 77301 | 0.69 | 0.697194 |
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Target: 5'- -aGACGUa-CUUGGCGUCG-GCCGGGg -3' miRNA: 3'- ccCUGCAgaGGAUCGCAGCuCGGUCU- -5' |
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| 28505 | 5' | -56.5 | NC_005946.1 | + | 38401 | 0.71 | 0.55317 |
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Target: 5'- aGGACGUCUgaggCCUuucgGGCGUCGAaCCAGc -3' miRNA: 3'- cCCUGCAGA----GGA----UCGCAGCUcGGUCu -5' |
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| 28505 | 5' | -56.5 | NC_005946.1 | + | 26972 | 0.71 | 0.533025 |
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Target: 5'- ---cCGUCUgCCUGGCGUCGGGCUuguGAa -3' miRNA: 3'- cccuGCAGA-GGAUCGCAGCUCGGu--CU- -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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