miRNA: 3'- -AGGCCC---UGGuaa-CGGUGG-------------UugUUUGU- -5'
miRNA: 3'- -AGGcCCuGGUaaCGGUGGUUGUuuGU- -5'
miRNA: 3'- -AGGcccuGGUAACGGUGGUUGUUUgu -5'
miRNA: 3'- -AGGCCCUGGUAACGGUGGUUGUUUGU- -5'
Results 1 - 4 of 4 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 | |||||||
| 15497 | 3' | -52.1 | NC_003992.2 | + | 7005 | 0.66 | 0.314468 |
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Target: 5'- cUCCGGGuuuACCuuggGCCACCcaggggaagcgccGugGAGCAc -3' miRNA: 3'- -AGGCCC---UGGuaa-CGGUGG-------------UugUUUGU- -5' |
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| 15497 | 3' | -52.1 | NC_003992.2 | + | 2239 | 0.66 | 0.28865 |
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Target: 5'- gUCCaGG-UCAgcGCCACCAGCAcuCAa -3' miRNA: 3'- -AGGcCCuGGUaaCGGUGGUUGUuuGU- -5' |
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| 15497 | 3' | -52.1 | NC_003992.2 | + | 6595 | 0.69 | 0.181165 |
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Target: 5'- aUCCaacuCCGUUGCCACCGGCGGAg- -3' miRNA: 3'- -AGGcccuGGUAACGGUGGUUGUUUgu -5' |
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| 15497 | 3' | -52.1 | NC_003992.2 | + | 2311 | 1.09 | 0.000119 |
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Target: 5'- uUCCGGGACCAUUGCCACCAACAAACAu -3' miRNA: 3'- -AGGCCCUGGUAACGGUGGUUGUUUGU- -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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