miRNA: 3'- guaaaGCUGUGGCGgu-UGGCC----AACCG- -5'
miRNA: 3'- guaaAGCUg---UGGCGGUUGG-------CCAACCG- -5'
miRNA: 3'- guaaagCUGUGgCGGUUGGCCaACCG- -5'
miRNA: 3'- guaaaGC---UGUGG-CGGUUGGCCAACCG- -5'
miRNA: 3'- -GUAAAGCUGUGGCGGUUGGCCAACCG- -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 | |||||||
| 3434 | 3' | -52.2 | NC_001600.1 | + | 3093 | 0.66 | 0.184914 |
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Target: 5'- ----aCGACGCCGCaauAUCGGggagUUGGUu -3' miRNA: 3'- guaaaGCUGUGGCGgu-UGGCC----AACCG- -5' |
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| 3434 | 3' | -52.2 | NC_001600.1 | + | 3024 | 0.67 | 0.140278 |
|
Target: 5'- ---gUCGAagcgAUCGUCAACCcaagccgGGUUGGCa -3' miRNA: 3'- guaaAGCUg---UGGCGGUUGG-------CCAACCG- -5' |
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| 3434 | 3' | -52.2 | NC_001600.1 | + | 1980 | 0.72 | 0.062307 |
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Target: 5'- -----aGACGCaGCCAGCUGG-UGGCa -3' miRNA: 3'- guaaagCUGUGgCGGUUGGCCaACCG- -5' |
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| 3434 | 3' | -52.2 | NC_001600.1 | + | 452 | 0.78 | 0.017285 |
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Target: 5'- ----aCGcaaACGCUaGCCAACCGGUUGGCg -3' miRNA: 3'- guaaaGC---UGUGG-CGGUUGGCCAACCG- -5' |
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| 3434 | 3' | -52.2 | NC_001600.1 | + | 493 | 1.12 | 0.000025 |
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Target: 5'- cCAUUUCGACACCGCCAACCGGUUGGCu -3' miRNA: 3'- -GUAAAGCUGUGGCGGUUGGCCAACCG- -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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