miRNA: 3'- -ACGGGGGCCUGGGUGUUUAUCAGGCA- -5'
miRNA: 3'- aCGGGG--GCCUGGGUGuUUA----------UCAGGCa -5'
miRNA: 3'- aCG--GgGGCCUGGGUGUUUAuCAgGCA- -5'
miRNA: 3'- aCGGG-GGCCU---GGGUGUUuaucaGGCA- -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 | |||||||
| 7593 | 5' | -57 | NC_001963.1 | + | 1906 | 1.08 | 0.000021 |
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Target: 5'- uUGCCCCCGGACCCACAAAUAGUCCGUa -3' miRNA: 3'- -ACGGGGGCCUGGGUGUUUAUCAGGCA- -5' |
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| 7593 | 5' | -57 | NC_001963.1 | + | 5154 | 0.71 | 0.034737 |
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Target: 5'- gGCCCCagCGGGCCCACuAGUauguugccccGGUCUGg -3' miRNA: 3'- aCGGGG--GCCUGGGUGuUUA----------UCAGGCa -5' |
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| 7593 | 5' | -57 | NC_001963.1 | + | 4459 | 0.67 | 0.071946 |
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Target: 5'- cGUaaUgCCGGGCCCACGAGUcGUgCGUa -3' miRNA: 3'- aCG--GgGGCCUGGGUGUUUAuCAgGCA- -5' |
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| 7593 | 5' | -57 | NC_001963.1 | + | 2075 | 0.66 | 0.094498 |
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Target: 5'- gGCCCaCCGGAcgcCCCGCAAcaa--CCGUg -3' miRNA: 3'- aCGGG-GGCCU---GGGUGUUuaucaGGCA- -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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