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miRNA: 3'- -GUCGCGUGUUUAGGGGCCCGACGGUG- -5'
miRNA: 3'- -GUCGCGUGUUUAgGGGC-CCG------------ACGGUG- -5'
miRNA: 3'- gUCGCGUgUuUAGGGGc-----CCgACGGUG- -5'
miRNA: 3'- gUCGCGugUUUA---GGGGCCCgaCGGUG- -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#
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P value |
| Predicted miRNA align pattern | |||||||
| 12740 | 3' | -58.8 | NC_003356.1 | + | 37266 | 1.08 | 0.000317 |
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Target: 5'- cCAGCGCACAAAUCCCCGGGCUGCCACc -3' miRNA: 3'- -GUCGCGUGUUUAGGGGCCCGACGGUG- -5' |
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| 12740 | 3' | -58.8 | NC_003356.1 | + | 29696 | 0.69 | 0.25989 |
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Target: 5'- cCAGUGUACAGGUgCCUGuGGUgaauggcgaugaUGCCACu -3' miRNA: 3'- -GUCGCGUGUUUAgGGGC-CCG------------ACGGUG- -5' |
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| 12740 | 3' | -58.8 | NC_003356.1 | + | 40201 | 0.67 | 0.359608 |
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Target: 5'- uGGCGCAgGcAUCCCCauguccGGaUGCCACa -3' miRNA: 3'- gUCGCGUgUuUAGGGGc-----CCgACGGUG- -5' |
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| 12740 | 3' | -58.8 | NC_003356.1 | + | 22721 | 0.66 | 0.404482 |
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Target: 5'- uGGCGCugAAGUguaUUCCGGG--GCCACa -3' miRNA: 3'- gUCGCGugUUUA---GGGGCCCgaCGGUG- -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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