miRNA: 3'- -AGGGCGCC-CGCUGuACCAA---CGUCGcg -5'
miRNA: 3'- aGGGCGcC-C-GCUG-UACCaACGuCGCG- -5'
miRNA: 3'- aGGGCGCCCGCuGUacCaaCGUCGCG- -5'
miRNA: 3'- -AGGGCGcCCGCUGUA-------CCaACG-UCGCG- -5'
miRNA: 3'- aGGGCGCcCGCUGUaccaaCGUCGCG- -5'
Results 1 - 5 of 5 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 | |||||||
| 12241 | 5' | -59.3 | NC_003309.1 | + | 49004 | 0.66 | 0.462026 |
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Target: 5'- uUCCCGUGGcGCGAU-UGGUUcgaGUGGCa- -3' miRNA: 3'- -AGGGCGCC-CGCUGuACCAA---CGUCGcg -5' |
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| 12241 | 5' | -59.3 | NC_003309.1 | + | 15338 | 0.67 | 0.405658 |
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Target: 5'- aCCCGCaGcGuCGGCgAUGGcUGCuGCGCg -3' miRNA: 3'- aGGGCGcC-C-GCUG-UACCaACGuCGCG- -5' |
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| 12241 | 5' | -59.3 | NC_003309.1 | + | 13636 | 0.68 | 0.362124 |
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Target: 5'- gUCCGCGGGCG-CGaaGcgGCGGCGUc -3' miRNA: 3'- aGGGCGCCCGCuGUacCaaCGUCGCG- -5' |
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| 12241 | 5' | -59.3 | NC_003309.1 | + | 16027 | 0.68 | 0.352993 |
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Target: 5'- cUUCCGC-GGCGGCGUagucaucGGaUGCgAGCGCg -3' miRNA: 3'- -AGGGCGcCCGCUGUA-------CCaACG-UCGCG- -5' |
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| 12241 | 5' | -59.3 | NC_003309.1 | + | 11989 | 0.72 | 0.216116 |
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Target: 5'- gCCCGCGcGCGGCAgcc--GCGGCGCg -3' miRNA: 3'- aGGGCGCcCGCUGUaccaaCGUCGCG- -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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