miRNA: 3'- caUGGCGag-UCGUUGU--UCGguCgUCG- -5'
miRNA: 3'- cAUG-GCGAGUCGUUgUUCGGucGUCG- -5'
miRNA: 3'- caUGGCGa----GUCGuugUUCGguCGUCG- -5'
miRNA: 3'- caUGGcGAGUCGUUGU-UCGGUCGUCG- -5'
miRNA: 3'- -CAUGGCGAGUCGUUGUUCGGUCGUCG- -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 | |||||||
| 9528 | 3' | -53.9 | NC_002534.1 | + | 2382 | 0.66 | 0.366953 |
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Target: 5'- -gGCCGCgggGGCGGCGuuGGCguGgGGCa -3' miRNA: 3'- caUGGCGag-UCGUUGU--UCGguCgUCG- -5' |
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| 9528 | 3' | -53.9 | NC_002534.1 | + | 3370 | 0.67 | 0.285849 |
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Target: 5'- uUGCuCGCUCGGUGGgGGGCCcaCGGCg -3' miRNA: 3'- cAUG-GCGAGUCGUUgUUCGGucGUCG- -5' |
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| 9528 | 3' | -53.9 | NC_002534.1 | + | 2354 | 0.69 | 0.233057 |
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Target: 5'- -cGCCGCccccgCGGCca-AAGCguGCAGCa -3' miRNA: 3'- caUGGCGa----GUCGuugUUCGguCGUCG- -5' |
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| 9528 | 3' | -53.9 | NC_002534.1 | + | 12237 | 0.74 | 0.091226 |
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Target: 5'- -aGCC-UUCGGUAGCAcGGCCGGCAGUg -3' miRNA: 3'- caUGGcGAGUCGUUGU-UCGGUCGUCG- -5' |
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| 9528 | 3' | -53.9 | NC_002534.1 | + | 2000 | 1.13 | 8.1e-05 |
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Target: 5'- aGUACCGCUCAGCAACAAGCCAGCAGCg -3' miRNA: 3'- -CAUGGCGAGUCGUUGUUCGGUCGUCG- -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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