miRNA: 3'- -UGUGGAu------------GCUCACCUUGa---AGGCGuuc -5'
miRNA: 3'- uGUGGa-UGCUCaCCUUGAaGGCGUUC- -5'
miRNA: 3'- -UGUGGAUGCUCAc---CUUGaaGGCGUuc -5'
miRNA: 3'- -UGUGGAUGCUCACCUUGAAGGCGUUC- -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 | |||||||
| 139 | 3' | -51.3 | AC_000006.1 | + | 23919 | 0.66 | 0.804416 |
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Target: 5'- cGCGCCUcgcccuucaggguCGAGUGGAGCacugUCUGCc-- -3' miRNA: 3'- -UGUGGAu------------GCUCACCUUGa---AGGCGuuc -5' |
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| 139 | 3' | -51.3 | AC_000006.1 | + | 4861 | 0.66 | 0.777323 |
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Target: 5'- cCGCCcaGCGAGaGGAGCUcUUGCAGGg -3' miRNA: 3'- uGUGGa-UGCUCaCCUUGAaGGCGUUC- -5' |
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| 139 | 3' | -51.3 | AC_000006.1 | + | 19234 | 0.75 | 0.293088 |
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Target: 5'- aACACCUACGAGUacauGAACggCCGCGu- -3' miRNA: 3'- -UGUGGAUGCUCAc---CUUGaaGGCGUuc -5' |
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| 139 | 3' | -51.3 | AC_000006.1 | + | 19474 | 1.1 | 0.001272 |
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Target: 5'- uACACCUACGAGUGGAACUUCCGCAAGg -3' miRNA: 3'- -UGUGGAUGCUCACCUUGAAGGCGUUC- -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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