miRNA: 3'- -GUCGaGCGAUAGgUGCucGAUU----UCUG- -5'
miRNA: 3'- -GUCG------AGCG-AUAGGUGCU-CGAuUUCUG- -5'
miRNA: 3'- gUCGA-GCGauaGGUGCUCGAUUu--CUG- -5'
miRNA: 3'- gUCGAGCGaUAGGUGCU-CGau-----UUCUG- -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 | |||||||
| 22140 | 5' | -50.8 | NC_004927.1 | + | 68021 | 0.66 | 0.952219 |
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Target: 5'- aCAGCcCGCUGUUgGCGucCUGAuggaGGACg -3' miRNA: 3'- -GUCGaGCGAUAGgUGCucGAUU----UCUG- -5' |
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| 22140 | 5' | -50.8 | NC_004927.1 | + | 60327 | 0.67 | 0.92043 |
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Target: 5'- uUAGCaucgagUCGCuUAUCUACGAuGCUcAGGGCg -3' miRNA: 3'- -GUCG------AGCG-AUAGGUGCU-CGAuUUCUG- -5' |
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| 22140 | 5' | -50.8 | NC_004927.1 | + | 17917 | 0.7 | 0.777907 |
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Target: 5'- aGGCUcCGUg--CCACGAGCUGAuguGAUu -3' miRNA: 3'- gUCGA-GCGauaGGUGCUCGAUUu--CUG- -5' |
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| 22140 | 5' | -50.8 | NC_004927.1 | + | 55038 | 0.75 | 0.492965 |
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Target: 5'- aAGCUCGCcGUCCACGGuGCgacguguGAGGCu -3' miRNA: 3'- gUCGAGCGaUAGGUGCU-CGau-----UUCUG- -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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