miRNA: 3'- -ACCUGaAGUGUgUUug--UGCG------AAUGGG- -5'
miRNA: 3'- -ACCUGAA-------------GUGUGUUUGU--GCGaa--UGGG- -5'
miRNA: 3'- aCCUGAAGUGUguu---UGugC-GAAUGGG- -5'
miRNA: 3'- -ACCUGAAGUGUGUUUGUGCGAAUGGG- -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 | |||||||
| 17790 | 3' | -47.9 | NC_004650.1 | + | 1670 | 0.67 | 0.207812 |
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Target: 5'- uUGGACaUCGCAgAAuauaGCGUuugcugUUGCCCa -3' miRNA: 3'- -ACCUGaAGUGUgUUug--UGCG------AAUGGG- -5' |
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| 17790 | 3' | -47.9 | NC_004650.1 | + | 1936 | 0.67 | 0.199853 |
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Target: 5'- uUGGGCUUagaucuaaaugccCACACAAAUAauUGUgaggGCCCa -3' miRNA: 3'- -ACCUGAA-------------GUGUGUUUGU--GCGaa--UGGG- -5' |
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| 17790 | 3' | -47.9 | NC_004650.1 | + | 569 | 0.73 | 0.068011 |
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Target: 5'- cGGAUUUUACAagggguACugGgCUUACCCa -3' miRNA: 3'- aCCUGAAGUGUguu---UGugC-GAAUGGG- -5' |
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| 17790 | 3' | -47.9 | NC_004650.1 | + | 634 | 1.15 | 2.4e-05 |
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Target: 5'- aUGGACUUCACACAAACACGCUUACCCa -3' miRNA: 3'- -ACCUGAAGUGUGUUUGUGCGAAUGGG- -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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