miRNA: 3'- aCCCCu--------------UUAUCAGGGGg---GGGUu-GGCc -5'
miRNA: 3'- -ACCCCU--------------UUAUCaGGGGGGGGu---UGgCC- -5'
miRNA: 3'- -ACCCCuuUauc----AGGGG-GGGGU-UGgCC- -5'
miRNA: 3'- -ACCCCUUUAUCAGGGGGGGGUUGGCC- -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 | |||||||
| 3438 | 5' | -57.5 | NC_001600.1 | + | 4016 | 0.66 | 0.076402 |
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Target: 5'- aGGGGcuauuuucuucauuuGGUGGUCCCCaacaCCCAcuCCGa -3' miRNA: 3'- aCCCCu--------------UUAUCAGGGGg---GGGUu-GGCc -5' |
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| 3438 | 5' | -57.5 | NC_001600.1 | + | 3982 | 0.66 | 0.067934 |
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Target: 5'- uUGGGGAccacaaaugaagaaAAUAG-CCCCUCCCucgcGCaGGg -3' miRNA: 3'- -ACCCCU--------------UUAUCaGGGGGGGGu---UGgCC- -5' |
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| 3438 | 5' | -57.5 | NC_001600.1 | + | 187 | 0.7 | 0.030682 |
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Target: 5'- uUGGGGggGgacuauuUCCCCaCCCCAuACgGGg -3' miRNA: 3'- -ACCCCuuUauc----AGGGG-GGGGU-UGgCC- -5' |
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| 3438 | 5' | -57.5 | NC_001600.1 | + | 162 | 1.11 | 8e-06 |
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Target: 5'- gUGGGGAAAUAGUCCCCCCCCAACCGGa -3' miRNA: 3'- -ACCCCUUUAUCAGGGGGGGGUUGGCC- -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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