miRNA: 3'- cacAAGGGCCUCGac---AAGGGCGU----GGU- -5'
miRNA: 3'- caCAAGGGC-CUCGACaAGGGcg-------UGGU- -5'
miRNA: 3'- caCAAGGGCCUCGacaagGGCGUGGU- -5'
miRNA: 3'- caCA--AGGGC-CUCGACAAGGGCgUGGU- -5'
miRNA: 3'- -CACAAGGGCCUCGACAAGGGCGUGGU- -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 | |||||||
| 1391 | 3' | -57.7 | NC_001335.1 | + | 33144 | 0.66 | 0.565595 |
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Target: 5'- --cUUCCCGGAGUccagcUUCCCGCAggcuCCGu -3' miRNA: 3'- cacAAGGGCCUCGac---AAGGGCGU----GGU- -5' |
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| 1391 | 3' | -57.7 | NC_001335.1 | + | 14844 | 0.67 | 0.491898 |
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Target: 5'- -gGUUCCCGaGGGCUGaUCCCaacuugacaGCCAc -3' miRNA: 3'- caCAAGGGC-CUCGACaAGGGcg-------UGGU- -5' |
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| 1391 | 3' | -57.7 | NC_001335.1 | + | 36833 | 0.67 | 0.471638 |
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Target: 5'- -gGUUCCUGGAGCcg---CUGCGCCAg -3' miRNA: 3'- caCAAGGGCCUCGacaagGGCGUGGU- -5' |
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| 1391 | 3' | -57.7 | NC_001335.1 | + | 38017 | 0.7 | 0.311689 |
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Target: 5'- -cGUacUUCCGaGAGCUGUUCCUGgGCUAc -3' miRNA: 3'- caCA--AGGGC-CUCGACAAGGGCgUGGU- -5' |
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| 1391 | 3' | -57.7 | NC_001335.1 | + | 35381 | 1.08 | 0.000588 |
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Target: 5'- gGUGUUCCCGGAGCUGUUCCCGCACCAg -3' miRNA: 3'- -CACAAGGGCCUCGACAAGGGCGUGGU- -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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