miRNA: 3'- uGUGCU---GGUGC---UAUUGGCG-GUUCUGU- -5'
miRNA: 3'- ugugCUGGUGC-------UAUU-GGCGGUUCUGU- -5'
miRNA: 3'- -UGUGCUGGUG---CUAU-----UGGCGGU---UCUGu -5'
miRNA: 3'- -UGUGCUGGUGCUAUUGGCGGUUCUGU- -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 | |||||||
| 22462 | 3' | -51.8 | NC_005064.1 | + | 5328 | 0.66 | 0.42629 |
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Target: 5'- uCAUGGaccCCAUGucaAUAGCCGCuCGAGGCAu -3' miRNA: 3'- uGUGCU---GGUGC---UAUUGGCG-GUUCUGU- -5' |
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| 22462 | 3' | -51.8 | NC_005064.1 | + | 1199 | 0.68 | 0.32444 |
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Target: 5'- ---gGGCCAUGuccaaauGUGAuCCGCCAGGGCAa -3' miRNA: 3'- ugugCUGGUGC-------UAUU-GGCGGUUCUGU- -5' |
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| 22462 | 3' | -51.8 | NC_005064.1 | + | 3668 | 0.7 | 0.229099 |
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Target: 5'- cGCGCGGCCGCaaaGAUGaugauGCUGCCAacaAGACc -3' miRNA: 3'- -UGUGCUGGUG---CUAU-----UGGCGGU---UCUGu -5' |
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| 22462 | 3' | -51.8 | NC_005064.1 | + | 6453 | 1.09 | 0.000263 |
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Target: 5'- cACACGACCACGAUAACCGCCAAGACAa -3' miRNA: 3'- -UGUGCUGGUGCUAUUGGCGGUUCUGU- -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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