miRNA: 3'- aGCCuGCaCGAAGAGGG--------UGGCGGGGU- -5'
miRNA: 3'- aGCCUGCA---------------CGaa------GAGGGUGgCGGGGU- -5'
miRNA: 3'- -AGCCUGCACGAAGAGGGUGGCGGGGU- -5'
miRNA: 3'- agC-CUGCACGA---AGAGGGUGGcGGGGu -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 |
| Predicted miRNA align pattern | |||||||
| 22045 | 5' | -60.3 | NC_004927.1 | + | 35563 | 0.68 | 0.435816 |
|
Target: 5'- aCGG-CGaGCUUCUUCCcguuacgaACCGCUCCGa -3' miRNA: 3'- aGCCuGCaCGAAGAGGG--------UGGCGGGGU- -5' |
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| 22045 | 5' | -60.3 | NC_004927.1 | + | 28571 | 0.7 | 0.337937 |
|
Target: 5'- gCGGAUGUgagguucgagccauuGCgcccaaucCUCCCACgGCCCCAu -3' miRNA: 3'- aGCCUGCA---------------CGaa------GAGGGUGgCGGGGU- -5' |
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| 22045 | 5' | -60.3 | NC_004927.1 | + | 22282 | 1.08 | 0.000596 |
|
Target: 5'- uUCGGACGUGCUUCUCCCACCGCCCCAu -3' miRNA: 3'- -AGCCUGCACGAAGAGGGUGGCGGGGU- -5' |
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| 22045 | 5' | -60.3 | NC_004927.1 | + | 6373 | 0.69 | 0.350446 |
|
Target: 5'- -aGaGGCGUGCUucaUCUCCCACUuCCCUc -3' miRNA: 3'- agC-CUGCACGA---AGAGGGUGGcGGGGu -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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