miRNA: 3'- uAUGUGGACUGGcGGGaGUAGGCCUg -5'
miRNA: 3'- -UAUGUGGACu-GGCGGGa--------GUAGGCcUG- -5'
miRNA: 3'- uaUGUGG---ACUGGCGGGaGUAGGCCUg -5'
miRNA: 3'- -UAUGUGGACUGGCGGGAGUAGGCCUG- -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 | |||||||
| 10632 | 3' | -57.6 | NC_002702.1 | + | 8039 | 0.69 | 0.282478 |
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Target: 5'- cUGCGCCUGGCCuCUC-CAUUCGGGa -3' miRNA: 3'- uAUGUGGACUGGcGGGaGUAGGCCUg -5' |
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| 10632 | 3' | -57.6 | NC_002702.1 | + | 13253 | 0.69 | 0.268061 |
|
Target: 5'- aGUACACCUGcuCCGCCCcacacgugaCAUCCGuGCu -3' miRNA: 3'- -UAUGUGGACu-GGCGGGa--------GUAGGCcUG- -5' |
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| 10632 | 3' | -57.6 | NC_002702.1 | + | 15363 | 0.7 | 0.222258 |
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Target: 5'- -aACGCCagaUGGCCGUCUcCGUCCGGGg -3' miRNA: 3'- uaUGUGG---ACUGGCGGGaGUAGGCCUg -5' |
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| 10632 | 3' | -57.6 | NC_002702.1 | + | 10771 | 1.08 | 0.000317 |
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Target: 5'- uAUACACCUGACCGCCCUCAUCCGGACg -3' miRNA: 3'- -UAUGUGGACUGGCGGGAGUAGGCCUG- -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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