miRNA: 3'- gCU---UGAGcGCUGGGUGC-CCCUCAAua -5'
miRNA: 3'- -GCUUGAgCGCug------GGUGCCCCUCAaua -5'
miRNA: 3'- -GCU---UGAG-C-GCUGGGUGCCCCUCaaua -5'
miRNA: 3'- -GCUUGAGCGCUGGGUGCCCCUCAAUA- -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 | |||||||
| 7253 | 5' | -55.5 | NC_001900.1 | + | 35411 | 0.66 | 0.648593 |
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Target: 5'- aGAucuGCUC-CGACUCAUGcGGGAGUUc- -3' miRNA: 3'- gCU---UGAGcGCUGGGUGC-CCCUCAAua -5' |
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| 7253 | 5' | -55.5 | NC_001900.1 | + | 21118 | 0.69 | 0.507022 |
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Target: 5'- uCGGGCUgGUGcccaggaaCCACGGGGAGUa-- -3' miRNA: 3'- -GCUUGAgCGCug------GGUGCCCCUCAaua -5' |
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| 7253 | 5' | -55.5 | NC_001900.1 | + | 48136 | 0.7 | 0.455841 |
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Target: 5'- cCGAuagAUUCuGuUGACCCACGGGGAGa--- -3' miRNA: 3'- -GCU---UGAG-C-GCUGGGUGCCCCUCaaua -5' |
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| 7253 | 5' | -55.5 | NC_001900.1 | + | 105 | 1.07 | 0.001201 |
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Target: 5'- aCGAACUCGCGACCCACGGGGAGUUAUa -3' miRNA: 3'- -GCUUGAGCGCUGGGUGCCCCUCAAUA- -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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