miRNA: 3'- -UGCGUCGa--UCCGGgcaugUCGGCU--UG- -5'
miRNA: 3'- ugCGUCga----UCCGGG-CAUG--UCGGCuUG- -5'
miRNA: 3'- uGC-GUCGAUCCGGGCa---UGUCggCu----UG- -5'
miRNA: 3'- ugCGUCG---AUCCGGGCAUGu-CGgCUUG- -5'
miRNA: 3'- uGCGUCGAu-----CCgGGCAUGUCGGCUUG- -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 | |||||||
| 8888 | 3' | -57.6 | NC_002484.1 | + | 44976 | 0.66 | 0.559517 |
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Target: 5'- aACGCAGCgccAGGCCaccg-AGCCGAccGCu -3' miRNA: 3'- -UGCGUCGa--UCCGGgcaugUCGGCU--UG- -5' |
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| 8888 | 3' | -57.6 | NC_002484.1 | + | 27746 | 0.66 | 0.538139 |
|
Target: 5'- -gGCAGaggucgAGGCCCuGUGCcgAGCCGcGCg -3' miRNA: 3'- ugCGUCga----UCCGGG-CAUG--UCGGCuUG- -5' |
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| 8888 | 3' | -57.6 | NC_002484.1 | + | 13407 | 0.69 | 0.372298 |
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Target: 5'- cCGcCAGCUGGGCCUGgaagGCAGuuGcuuguGCg -3' miRNA: 3'- uGC-GUCGAUCCGGGCa---UGUCggCu----UG- -5' |
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| 8888 | 3' | -57.6 | NC_002484.1 | + | 5273 | 0.69 | 0.372298 |
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Target: 5'- -gGCGGCgcgUAGGCCUGUGCcuGCgGAAUg -3' miRNA: 3'- ugCGUCG---AUCCGGGCAUGu-CGgCUUG- -5' |
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| 8888 | 3' | -57.6 | NC_002484.1 | + | 52935 | 0.76 | 0.128381 |
|
Target: 5'- cCGCGGCUugagcuGG-CUGUGCAGCCGGGCg -3' miRNA: 3'- uGCGUCGAu-----CCgGGCAUGUCGGCUUG- -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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