miRNA: 3'- cUCuGAUCA----GGGCAG----UGGUUUUCUCg -5'
miRNA: 3'- cUCUGauCAGGGCa--GUGGUUU----UCUCG- -5'
miRNA: 3'- cuCUGAUCAG-GGc-----AGUGGU-------------UUUCUCG- -5'
miRNA: 3'- -CUCUGAUCAGGGCAGUGGUUUUCUCG- -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 | |||||||
| 14980 | 5' | -50 | NC_003690.1 | + | 5683 | 0.66 | 0.553231 |
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Target: 5'- cAGcCUGGUucguUCCGUCaauuGCCAGAGGAGg -3' miRNA: 3'- cUCuGAUCA----GGGCAG----UGGUUUUCUCg -5' |
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| 14980 | 5' | -50 | NC_003690.1 | + | 7194 | 0.67 | 0.491359 |
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Target: 5'- aAGACauGUCCCGccaCACCAAAgaaaGGAGUc -3' miRNA: 3'- cUCUGauCAGGGCa--GUGGUUU----UCUCG- -5' |
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| 14980 | 5' | -50 | NC_003690.1 | + | 3612 | 0.67 | 0.454641 |
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Target: 5'- -uGGCUGGUCgCCuucuaaUCACCAgcuccaaaaccacAAAGAGCg -3' miRNA: 3'- cuCUGAUCAG-GGc-----AGUGGU-------------UUUCUCG- -5' |
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| 14980 | 5' | -50 | NC_003690.1 | + | 3677 | 1.12 | 0.000234 |
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Target: 5'- aGAGACUAGUCCCGUCACCAAAAGAGCc -3' miRNA: 3'- -CUCUGAUCAGGGCAGUGGUUUUCUCG- -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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