miRNA: 3'- -AGAGUGCG-UUAcGCAuCGGCUGUUca -5'
miRNA: 3'- aGAGUGCGUu-ACGCAUCG-----GCUGUuca -5'
miRNA: 3'- aGAGUGCGU-------UACGCa-----UCGGCUGUUCA- -5'
miRNA: 3'- aGAGUGCGUUaCGCaUCGGC--UGUUCa -5'
miRNA: 3'- -AGAGUGCGUUACGCAUCGGCUGUUCA- -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 | |||||||
| 12177 | 5' | -51.6 | NC_003309.1 | + | 22732 | 0.68 | 0.766665 |
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Target: 5'- aUCUCGCGCuGAU-CGUcGCCGGCGAc- -3' miRNA: 3'- -AGAGUGCG-UUAcGCAuCGGCUGUUca -5' |
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| 12177 | 5' | -51.6 | NC_003309.1 | + | 10865 | 0.69 | 0.734488 |
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Target: 5'- gCUCGCGCGccUGCGUGGCaagcgCGACAu-- -3' miRNA: 3'- aGAGUGCGUu-ACGCAUCG-----GCUGUuca -5' |
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| 12177 | 5' | -51.6 | NC_003309.1 | + | 37494 | 0.69 | 0.688975 |
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Target: 5'- gUUCACGCAguccuacGUGUGggacaaAGCUGGCAAGUc -3' miRNA: 3'- aGAGUGCGU-------UACGCa-----UCGGCUGUUCA- -5' |
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| 12177 | 5' | -51.6 | NC_003309.1 | + | 2467 | 0.75 | 0.370234 |
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Target: 5'- aCUCGCGCAGcGCG-AGCCGccGCGAGa -3' miRNA: 3'- aGAGUGCGUUaCGCaUCGGC--UGUUCa -5' |
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| 12177 | 5' | -51.6 | NC_003309.1 | + | 45065 | 1.08 | 0.002456 |
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Target: 5'- aUCUCACGCAAUGCGUAGCCGACAAGUu -3' miRNA: 3'- -AGAGUGCGUUACGCAUCGGCUGUUCA- -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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