miRNA: 3'- gCUCGGUGGGCGUAGuUGGGcaAG-CG- -5'
miRNA: 3'- gCUCGGUG-GGCGua-GUUGGGCa--------------AGCG- -5'
miRNA: 3'- -GCUCGGugGGCG--UAgUUGGGCaa--GCG- -5'
miRNA: 3'- gCUCGGUGGG---CGu------AGU--UGGGC-AAGCG- -5'
miRNA: 3'- -GCUCGGUGGGCGUAGUUGGGCAAGCG- -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 | |||||||
| 31981 | 3' | -56.1 | NC_006948.1 | + | 2303 | 0.66 | 0.142712 |
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Target: 5'- gGGGUCACUCGUAUC-ACCCacUCuGCg -3' miRNA: 3'- gCUCGGUGGGCGUAGuUGGGcaAG-CG- -5' |
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| 31981 | 3' | -56.1 | NC_006948.1 | + | 1049 | 0.67 | 0.125682 |
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Target: 5'- uGAGCUGCaCCGCuacCAACCCGaagauguggugcacaUCGCc -3' miRNA: 3'- gCUCGGUG-GGCGua-GUUGGGCa--------------AGCG- -5' |
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| 31981 | 3' | -56.1 | NC_006948.1 | + | 2634 | 0.67 | 0.125271 |
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Target: 5'- cCGAGCCugUCGCccGUgAGCCUGaggcCGCc -3' miRNA: 3'- -GCUCGGugGGCG--UAgUUGGGCaa--GCG- -5' |
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| 31981 | 3' | -56.1 | NC_006948.1 | + | 5534 | 0.71 | 0.054206 |
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Target: 5'- uGGGCCGCCCaagGCuucccuuUCGaaGCCCGcUUCGCc -3' miRNA: 3'- gCUCGGUGGG---CGu------AGU--UGGGC-AAGCG- -5' |
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| 31981 | 3' | -56.1 | NC_006948.1 | + | 168 | 1.11 | 2.2e-05 |
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Target: 5'- cCGAGCCACCCGCAUCAACCCGUUCGCc -3' miRNA: 3'- -GCUCGGUGGGCGUAGUUGGGCAAGCG- -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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