miRNA: 3'- -CG-AGGCGGUa-------UGCUGCCaaaaGCCau -5'
miRNA: 3'- cgAGGCGGU----AUGCUGCCaa--------AAGCCau -5'
miRNA: 3'- cgaGGCG-GUAUGCUGCCAa---AAGCCAu -5'
miRNA: 3'- -CGAGGCGGUAUGCUGCCAAAAGCCAU- -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 | |||||||
| 12098 | 3' | -51.9 | NC_003309.1 | + | 53314 | 0.68 | 0.802021 |
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Target: 5'- cGCaUCCGCCGggcgggcaACGACGGg---CGGg- -3' miRNA: 3'- -CG-AGGCGGUa-------UGCUGCCaaaaGCCau -5' |
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| 12098 | 3' | -51.9 | NC_003309.1 | + | 15508 | 0.69 | 0.718445 |
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Target: 5'- -aUCCGCCAcugcUGCGGCGGcauuucuucgUUCGGg- -3' miRNA: 3'- cgAGGCGGU----AUGCUGCCaa--------AAGCCau -5' |
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| 12098 | 3' | -51.9 | NC_003309.1 | + | 9405 | 0.74 | 0.445152 |
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Target: 5'- --aCCGCgCAUGCGGCGGUcguaUUCGGUc -3' miRNA: 3'- cgaGGCG-GUAUGCUGCCAa---AAGCCAu -5' |
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| 12098 | 3' | -51.9 | NC_003309.1 | + | 1835 | 1.1 | 0.002029 |
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Target: 5'- cGCUCCGCCAUACGACGGUUUUCGGUAu -3' miRNA: 3'- -CGAGGCGGUAUGCUGCCAAAAGCCAU- -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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