miRNA: 3'- guCACCUGG--------------CAGUuaa-AGCUGCCUGG- -5'
miRNA: 3'- -GUCACCUGGCaGUuaaaGCUGCC-------------UGG- -5'
miRNA: 3'- -GUCACCUGG------------CAGUu-AAAGC--UGCCuGG- -5'
miRNA: 3'- -GUCaCCUGGCAGUUAA----------AGCUGCCU---GG- -5'
Results 21 - 24 of 24 are showing below:
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| ID | Location | Perfect MFE.* | RefSeq Acc. |
strand
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Start Position | R_P_ratio# | P value |
| Predicted miRNA align pattern | |||||||
| 2043 | 3' | -50.5 | NC_001347.2 | + | 149287 | 0.66 | 0.99888 |
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Target: 5'- -uGUGGAUCcgcugacgcguuugGUCAucgaUCGGCGGAUCa -3' miRNA: 3'- guCACCUGG--------------CAGUuaa-AGCUGCCUGG- -5' |
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| 2043 | 3' | -50.5 | NC_001347.2 | + | 1736 | 0.67 | 0.998139 |
|
Target: 5'- gCGGUGGGCCGgCA----CGACGGuggcgcugcagacGCCg -3' miRNA: 3'- -GUCACCUGGCaGUuaaaGCUGCC-------------UGG- -5' |
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| 2043 | 3' | -50.5 | NC_001347.2 | + | 24914 | 0.67 | 0.998172 |
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Target: 5'- aCGGUGGGCCuuaucuucgccgGUCAcuUUUCGcaGCGGuCCu -3' miRNA: 3'- -GUCACCUGG------------CAGUu-AAAGC--UGCCuGG- -5' |
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| 2043 | 3' | -50.5 | NC_001347.2 | + | 209961 | 0.78 | 0.746595 |
|
Target: 5'- cCAGcGGACCGUCAGUUguuggcguagUUGACGGAgucCCg -3' miRNA: 3'- -GUCaCCUGGCAGUUAA----------AGCUGCCU---GG- -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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