miRNA: 3'- aagaGCGCaCGGU-----GGUUGaGGUGGGG- -5'
miRNA: 3'- aAGAGCGCaCGGUg---GUUG-AGGUGGGG- -5'
miRNA: 3'- aAGaGCGCacGGUGGU---UGAGGUGGGG- -5'
miRNA: 3'- aAGaGCGcaCGGUGGUuGAGGUGGGG- -5'
miRNA: 3'- -AAGAGCGCACGGUGGUUGAGGUGGGG- -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 | |||||||
| 15291 | 3' | -57.8 | NC_003849.1 | + | 5934 | 0.66 | 0.103362 |
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Target: 5'- ---cCGUG-GCCAacucuCCAACaCCGCCCCa -3' miRNA: 3'- aagaGCGCaCGGU-----GGUUGaGGUGGGG- -5' |
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| 15291 | 3' | -57.8 | NC_003849.1 | + | 2724 | 0.66 | 0.099985 |
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Target: 5'- cUCUCGCGgGCCGuggaCAGCaUCCAUUUCg -3' miRNA: 3'- aAGAGCGCaCGGUg---GUUG-AGGUGGGG- -5' |
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| 15291 | 3' | -57.8 | NC_003849.1 | + | 2413 | 0.66 | 0.090468 |
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Target: 5'- cUCcCGCGa-CCACCAucuACUCCGCCUUc -3' miRNA: 3'- aAGaGCGCacGGUGGU---UGAGGUGGGG- -5' |
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| 15291 | 3' | -57.8 | NC_003849.1 | + | 4582 | 0.71 | 0.034901 |
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Target: 5'- gUC-CGUcaGCCACCGcCUCUGCCCCg -3' miRNA: 3'- aAGaGCGcaCGGUGGUuGAGGUGGGG- -5' |
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| 15291 | 3' | -57.8 | NC_003849.1 | + | 1401 | 1.1 | 0.000015 |
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Target: 5'- cUUCUCGCGUGCCACCAACUCCACCCCa -3' miRNA: 3'- -AAGAGCGCACGGUGGUUGAGGUGGGG- -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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