miRNA: 3'- -UC-GUuUCCaGGCUGCGGG----GUGUA----GCG- -5'
miRNA: 3'- uCGUUUCCa---GGCUGCGGGGUGuaGCG- -5'
miRNA: 3'- -UCGUu------UCCAGGCUGCG-GGGUguagCG- -5'
miRNA: 3'- -UC-GUUUCC-AGGCugCGGGGUGU---AGCG- -5'
miRNA: 3'- -UCGUUUCCAGGCUGCGGGGUGUAGCG- -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 | |||||||
| 9517 | 5' | -56 | NC_002532.2 | + | 1270 | 0.67 | 0.242927 |
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Target: 5'- gAGaCAcAGG-CCGACGCCCuuugCACGUuugaCGCg -3' miRNA: 3'- -UC-GUuUCCaGGCUGCGGG----GUGUA----GCG- -5' |
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| 9517 | 5' | -56 | NC_002532.2 | + | 2385 | 0.67 | 0.242927 |
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Target: 5'- cGUAGAGGcacaCUGACGCUCCAU--UGCg -3' miRNA: 3'- uCGUUUCCa---GGCUGCGGGGUGuaGCG- -5' |
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| 9517 | 5' | -56 | NC_002532.2 | + | 8168 | 0.7 | 0.146448 |
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Target: 5'- uGGCAcgcucgcGGGUCCGACGCaCCCGa---GCu -3' miRNA: 3'- -UCGUu------UCCAGGCUGCG-GGGUguagCG- -5' |
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| 9517 | 5' | -56 | NC_002532.2 | + | 5458 | 0.72 | 0.097767 |
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Target: 5'- aAGaCAAGGGuUUCGugGCUCUACAcagUCGCa -3' miRNA: 3'- -UC-GUUUCC-AGGCugCGGGGUGU---AGCG- -5' |
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| 9517 | 5' | -56 | NC_002532.2 | + | 5463 | 1.11 | 8e-05 |
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Target: 5'- cAGCAAAGGUCCGACGCCCCACAUCGCc -3' miRNA: 3'- -UCGUUUCCAGGCUGCGGGGUGUAGCG- -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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