miRNA: 3'- -CGAA---UG--UGGGUCAaaGGACAUUa -5'
miRNA: 3'- -CGAAuGUGGGUC---------------AAAGGACAUUA- -5'
miRNA: 3'- cgaAUGUGGGUCAaa-------GGACAUUA- -5'
miRNA: 3'- -CGaAUGUGgGUC-AAAGGACAUUA- -5'
miRNA: 3'- -CGAAUGUGGGUCAAAGGACAUUA- -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 | |||||||
| 13461 | 5' | -43.6 | NC_003409.1 | + | 65946 | 0.66 | 0.999991 |
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Target: 5'- aGCUUuucACcuGCCCAGUggUCUGUGAg -3' miRNA: 3'- -CGAA---UG--UGGGUCAaaGGACAUUa -5' |
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| 13461 | 5' | -43.6 | NC_003409.1 | + | 7623 | 0.67 | 0.999968 |
|
Target: 5'- uGCUUuCGCCCAGacucccuagaaacccUUUUCUGUGGUg -3' miRNA: 3'- -CGAAuGUGGGUC---------------AAAGGACAUUA- -5' |
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| 13461 | 5' | -43.6 | NC_003409.1 | + | 122185 | 0.67 | 0.999949 |
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Target: 5'- --gUACACCCAGUguaagaaugUCUGUGGUg -3' miRNA: 3'- cgaAUGUGGGUCAaa-------GGACAUUA- -5' |
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| 13461 | 5' | -43.6 | NC_003409.1 | + | 96830 | 0.68 | 0.999833 |
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Target: 5'- aGUgUGCGCgCAGcUUUCCUGUGAUu -3' miRNA: 3'- -CGaAUGUGgGUC-AAAGGACAUUA- -5' |
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| 13461 | 5' | -43.6 | NC_003409.1 | + | 121766 | 1.02 | 0.070328 |
|
Target: 5'- aGCUUACACCCAGUUUCCUGUAAUc -3' miRNA: 3'- -CGAAUGUGGGUCAAAGGACAUUA- -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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