miRNA: 3'- uGCGGuAGCGUCACCuCAaCGCGAuu -5'
miRNA: 3'- ugCGGUAGCGUCACc-----UCA--------ACGCGAUu -5'
miRNA: 3'- -UGCGGUAGCGUC------ACCUCaACGCGauu -5'
miRNA: 3'- -UGCGGUAGCGUCACCUCAACGCGAUU- -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 | |||||||
| 22336 | 3' | -55.3 | NC_005045.1 | + | 7100 | 0.68 | 0.474097 |
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Target: 5'- uCGCC-UCGCGGUGG-GUgGUGCUc- -3' miRNA: 3'- uGCGGuAGCGUCACCuCAaCGCGAuu -5' |
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| 22336 | 3' | -55.3 | NC_005045.1 | + | 3272 | 0.68 | 0.463629 |
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Target: 5'- -aGCCGUCGCGGUGcaugacGGUauaccacgUGCGCUGu -3' miRNA: 3'- ugCGGUAGCGUCACc-----UCA--------ACGCGAUu -5' |
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| 22336 | 3' | -55.3 | NC_005045.1 | + | 19477 | 0.81 | 0.063994 |
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Target: 5'- uGCGCCAUCGCAGgucugcUGGAGcUGCGCg-- -3' miRNA: 3'- -UGCGGUAGCGUC------ACCUCaACGCGauu -5' |
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| 22336 | 3' | -55.3 | NC_005045.1 | + | 20851 | 1.06 | 0.000927 |
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Target: 5'- gACGCCAUCGCAGUGGAGUUGCGCUAAu -3' miRNA: 3'- -UGCGGUAGCGUCACCUCAACGCGAUU- -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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