miRNA: 3'- -GUCGA----------GGGUCAGGAgACCaUCa--AGGa -5'
miRNA: 3'- -GUCGAGGGUCAGGA------------GACCaucaaGGa -5'
miRNA: 3'- gUC-GAGGGUC-AGGAGACCaUCAAGGa -5'
miRNA: 3'- gUCGa--GGGUCAGGAGACCAUCAagga -5'
miRNA: 3'- -GUCGAGGGUCAGGAGACCAUCAAGGA- -5'
Results 1 - 5 of 5 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 | |||||||
| 1333 | 5' | -55.6 | NC_001335.1 | + | 25136 | 0.67 | 0.57136 |
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Target: 5'- gCGGCUgccuucuucgCCCGGUCCUgUGG-AGgggUCCa -3' miRNA: 3'- -GUCGA----------GGGUCAGGAgACCaUCa--AGGa -5' |
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| 1333 | 5' | -55.6 | NC_001335.1 | + | 2389 | 0.68 | 0.538646 |
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Target: 5'- cCGGCUCCCGGUCCUuucugcugccaaCUGGcuuugCCa -3' miRNA: 3'- -GUCGAGGGUCAGGA------------GACCaucaaGGa -5' |
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| 1333 | 5' | -55.6 | NC_001335.1 | + | 30367 | 0.69 | 0.455122 |
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Target: 5'- aAGcCUUCCAGaUCCUCUGG-GGUUUCa -3' miRNA: 3'- gUC-GAGGGUC-AGGAGACCaUCAAGGa -5' |
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| 1333 | 5' | -55.6 | NC_001335.1 | + | 6873 | 0.7 | 0.406607 |
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Target: 5'- aGGUacgCCUGGUCCUCUGGUGGUa--- -3' miRNA: 3'- gUCGa--GGGUCAGGAGACCAUCAagga -5' |
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| 1333 | 5' | -55.6 | NC_001335.1 | + | 2435 | 1.08 | 0.000961 |
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Target: 5'- uCAGCUCCCAGUCCUCUGGUAGUUCCUg -3' miRNA: 3'- -GUCGAGGGUCAGGAGACCAUCAAGGA- -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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