miRNA: 3'- aGGCGCGAU--CUGu--UGGCgaGCAgAUG- -5'
miRNA: 3'- aGGCG-CGa---UCuGUUGGCGAGCAG-AUG- -5'
miRNA: 3'- agGCGCGAUCUGU-------UGGCG--AGCaGAUG- -5'
miRNA: 3'- -AGGCGCGAUCUGUUGGCGAGCAGAUG- -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 | |||||||
| 15403 | 5' | -54.5 | NC_003907.2 | + | 19935 | 0.66 | 0.713669 |
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Target: 5'- gCCGUGCUGuuGGCuacACCGgaCGUgUGCa -3' miRNA: 3'- aGGCGCGAU--CUGu--UGGCgaGCAgAUG- -5' |
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| 15403 | 5' | -54.5 | NC_003907.2 | + | 26129 | 0.67 | 0.658211 |
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Target: 5'- aCCGCaGCggugAGcUGGCUGCUCGUCgUGCu -3' miRNA: 3'- aGGCG-CGa---UCuGUUGGCGAGCAG-AUG- -5' |
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| 15403 | 5' | -54.5 | NC_003907.2 | + | 34688 | 0.69 | 0.53466 |
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Target: 5'- -gUGCGCUGGACAguuaaggACCGUccUCG-CUGCu -3' miRNA: 3'- agGCGCGAUCUGU-------UGGCG--AGCaGAUG- -5' |
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| 15403 | 5' | -54.5 | NC_003907.2 | + | 43850 | 1.11 | 0.000664 |
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Target: 5'- aUCCGCGCUAGACAACCGCUCGUCUACa -3' miRNA: 3'- -AGGCGCGAUCUGUUGGCGAGCAGAUG- -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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