miRNA: 3'- gCGa-GCCGU------UGGaCGACGACUCaauu -5'
miRNA: 3'- -GCG-AGCCG-UUGGACGacGACUCAauu -5'
miRNA: 3'- gCGa-GCCGUU---GGACGa--CGACUCAAUU- -5'
miRNA: 3'- gCG-AGCCGu----UGGACGa----CGACUCAAuu -5'
miRNA: 3'- -GCGAGCCGUUGGACGACGACUCAAUU- -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 | |||||||
| 12293 | 5' | -54.3 | NC_003313.1 | + | 17657 | 0.66 | 0.555266 |
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Target: 5'- aGCagCGGCAugagcuGCC-GCUGCUGGGg--- -3' miRNA: 3'- gCGa-GCCGU------UGGaCGACGACUCaauu -5' |
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| 12293 | 5' | -54.3 | NC_003313.1 | + | 18524 | 0.66 | 0.532372 |
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Target: 5'- uCGCaUCGGUaAACCUGCaaCUGAGUg-- -3' miRNA: 3'- -GCG-AGCCG-UUGGACGacGACUCAauu -5' |
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| 12293 | 5' | -54.3 | NC_003313.1 | + | 20910 | 0.67 | 0.509826 |
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Target: 5'- uGCagCGGCGAugcUCUGCggcGUUGAGUUGAg -3' miRNA: 3'- gCGa-GCCGUU---GGACGa--CGACUCAAUU- -5' |
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| 12293 | 5' | -54.3 | NC_003313.1 | + | 22708 | 0.67 | 0.498704 |
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Target: 5'- uGCuUUGGUuagcuGCCUGCgcuugGCUGAGUUu- -3' miRNA: 3'- gCG-AGCCGu----UGGACGa----CGACUCAAuu -5' |
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| 12293 | 5' | -54.3 | NC_003313.1 | + | 11462 | 1.07 | 0.000648 |
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Target: 5'- aCGCUCGGCAACCUGCUGCUGAGUUAAg -3' miRNA: 3'- -GCGAGCCGUUGGACGACGACUCAAUU- -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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