miRNA: 3'- -AUCACgagGUCaCUGCUGAAGUGGGu -5'
miRNA: 3'- aUCACGAGGUCaCUGC--UGA----AGugGGU- -5'
miRNA: 3'- aUCACGA------------Gg------UCACUGCU-GAAGUGGGU- -5'
miRNA: 3'- aucaCGAGGUCa-----CUGCUGAAGUGGGU- -5'
miRNA: 3'- -AUCACGAGGUCACUGCUGAAGUGGGU- -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 | |||||||
| 12719 | 3' | -54.2 | NC_003356.1 | + | 41868 | 0.66 | 0.643696 |
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Target: 5'- aUGGUGaa-CGG-GGCGAUUUCGCCCc -3' miRNA: 3'- -AUCACgagGUCaCUGCUGAAGUGGGu -5' |
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| 12719 | 3' | -54.2 | NC_003356.1 | + | 6973 | 0.67 | 0.57522 |
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Target: 5'- aGGUGUUCCAGaGGCGuaGCUauucUCugCCAu -3' miRNA: 3'- aUCACGAGGUCaCUGC--UGA----AGugGGU- -5' |
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| 12719 | 3' | -54.2 | NC_003356.1 | + | 18946 | 0.67 | 0.57522 |
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Target: 5'- aAGUGCUgaguuauuugagCaaaguaaAGUGAUGAuCUUCACCCAa -3' miRNA: 3'- aUCACGA------------Gg------UCACUGCU-GAAGUGGGU- -5' |
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| 12719 | 3' | -54.2 | NC_003356.1 | + | 16424 | 0.77 | 0.147397 |
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Target: 5'- ---cGUUCCAGcguccgGACGGCUUCGCCCAg -3' miRNA: 3'- aucaCGAGGUCa-----CUGCUGAAGUGGGU- -5' |
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| 12719 | 3' | -54.2 | NC_003356.1 | + | 12457 | 1.07 | 0.000998 |
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Target: 5'- aUAGUGCUCCAGUGACGACUUCACCCAg -3' miRNA: 3'- -AUCACGAGGUCACUGCUGAAGUGGGU- -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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