miRNA: 3'- cGUC--UGUGGUGGg---ACCuGUa---CUAGUC- -5'
miRNA: 3'- -CGUCUGU-GGUgGGACCuGUaCUAGUc -5'
miRNA: 3'- -CG-UCUGUgGUGGG--ACCUGuaCUAGUC- -5'
miRNA: 3'- -CGUCUGUgGUGGGACCUGUACUAGUC- -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 | |||||||
| 13619 | 3' | -53 | NC_003460.1 | + | 3111 | 0.66 | 0.206792 |
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Target: 5'- cCAGgcACACCACCaggaUGGuCAgggcGAUCAGg -3' miRNA: 3'- cGUC--UGUGGUGGg---ACCuGUa---CUAGUC- -5' |
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| 13619 | 3' | -53 | NC_003460.1 | + | 5559 | 0.68 | 0.134693 |
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Target: 5'- cGCGGACAgCCA-CCUGGcCAcGAUCAc -3' miRNA: 3'- -CGUCUGU-GGUgGGACCuGUaCUAGUc -5' |
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| 13619 | 3' | -53 | NC_003460.1 | + | 4280 | 0.72 | 0.072606 |
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Target: 5'- aGCgAGGCG-CACCUugUGGACcgGAUCAGg -3' miRNA: 3'- -CG-UCUGUgGUGGG--ACCUGuaCUAGUC- -5' |
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| 13619 | 3' | -53 | NC_003460.1 | + | 3817 | 0.99 | 0.000409 |
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Target: 5'- cGCAGACA-CACCCUGGACAUGAUCAGg -3' miRNA: 3'- -CGUCUGUgGUGGGACCUGUACUAGUC- -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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