miRNA: 3'- cuCCAUGa----G-GGUGCaGCG----------CUCCACCU- -5'
miRNA: 3'- cUCCAUGaGGGUGCaGCGCUCCaccu -5'
miRNA: 3'- cuCCAUGAG--------------GGUGCAGcGcUCCACCU- -5'
miRNA: 3'- -CUCCa--UGAgG-GugCAgCGCUCC-ACCU- -5'
miRNA: 3'- -CUCCAUGAGGGUGCAGCGCUCCACCU- -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 | |||||||
| 11473 | 5' | -57.6 | NC_003085.1 | + | 15197 | 0.66 | 0.574719 |
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Target: 5'- -cGGUGCgccagCgCCGCGcCGCggaagugggcGAGGUGGAc -3' miRNA: 3'- cuCCAUGa----G-GGUGCaGCG----------CUCCACCU- -5' |
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| 11473 | 5' | -57.6 | NC_003085.1 | + | 16197 | 0.66 | 0.574719 |
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Target: 5'- cAGGUACgCUCGCG-CGCGAGGa--- -3' miRNA: 3'- cUCCAUGaGGGUGCaGCGCUCCaccu -5' |
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| 11473 | 5' | -57.6 | NC_003085.1 | + | 21184 | 0.67 | 0.528988 |
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Target: 5'- -uGGUACUCgccgcuccacacguCCACGUC-CcAGGUGGAg -3' miRNA: 3'- cuCCAUGAG--------------GGUGCAGcGcUCCACCU- -5' |
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| 11473 | 5' | -57.6 | NC_003085.1 | + | 3647 | 0.68 | 0.450912 |
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Target: 5'- aGAGGgacGCUgCaCugGUgGCGAGGuUGGAg -3' miRNA: 3'- -CUCCa--UGAgG-GugCAgCGCUCC-ACCU- -5' |
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| 11473 | 5' | -57.6 | NC_003085.1 | + | 19778 | 1.08 | 0.000664 |
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Target: 5'- gGAGGUACUCCCACGUCGCGAGGUGGAc -3' miRNA: 3'- -CUCCAUGAGGGUGCAGCGCUCCACCU- -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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