miRNA: 3'- acaACUGGACggUCAUuaUGGCGGUa -5'
miRNA: 3'- acaaCUGGACGGUCa---UUAUGGCGGUa -5'
miRNA: 3'- -ACAACugGa-CGGUcAUUAUGGCGGUa -5'
miRNA: 3'- acaACUGGACGGUCA----UUA----UGG-CGGUa -5'
miRNA: 3'- -ACAACUGGACGGUCAUUAUGGCGGUA- -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 | |||||||
| 13558 | 3' | -52 | NC_003444.1 | + | 15317 | 0.66 | 0.707858 |
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Target: 5'- --aUGGCCUGaaGGUG--ACCGCCGg -3' miRNA: 3'- acaACUGGACggUCAUuaUGGCGGUa -5' |
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| 13558 | 3' | -52 | NC_003444.1 | + | 36473 | 0.67 | 0.696273 |
|
Target: 5'- ---aGGCUUGCUGGcaacGGUACCGCCGg -3' miRNA: 3'- acaaCUGGACGGUCa---UUAUGGCGGUa -5' |
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| 13558 | 3' | -52 | NC_003444.1 | + | 5090 | 0.69 | 0.566995 |
|
Target: 5'- gUGUUGugCcgGUCAcUGAUGCUGCCAg -3' miRNA: 3'- -ACAACugGa-CGGUcAUUAUGGCGGUa -5' |
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| 13558 | 3' | -52 | NC_003444.1 | + | 631 | 0.71 | 0.434099 |
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Target: 5'- --gUGGCCUGCCAGUuuguGAUucagGCCuGCCAg -3' miRNA: 3'- acaACUGGACGGUCA----UUA----UGG-CGGUa -5' |
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| 13558 | 3' | -52 | NC_003444.1 | + | 16542 | 1.06 | 0.001701 |
|
Target: 5'- aUGUUGACCUGCCAGUAAUACCGCCAUu -3' miRNA: 3'- -ACAACUGGACGGUCAUUAUGGCGGUA- -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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