miRNA: 3'- -UCUCAUGAggCGGCCAUuAUUugGGg -5'
miRNA: 3'- -UCUcAUGAGGCGGCCAuuAUUUGg----GG- -5'
miRNA: 3'- -UCuCAuGAGGCGGCCAUUauUUGgGG- -5'
miRNA: 3'- uCUCAUG---AGG--CGGCCAUUAUuUGGGG- -5'
miRNA: 3'- -UCUCAUGAGGCGGCCAUUAUUUGGGG- -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 | |||||||
| 27332 | 3' | -50.4 | NC_005857.1 | + | 8383 | 0.66 | 0.938325 |
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Target: 5'- uGGGGUACU--GCCGGUGcUAAugCUg -3' miRNA: 3'- -UCUCAUGAggCGGCCAUuAUUugGGg -5' |
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| 27332 | 3' | -50.4 | NC_005857.1 | + | 50401 | 0.66 | 0.914694 |
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Target: 5'- gAGAaUGCUCCGCUGGU--UGAGCguuugCCg -3' miRNA: 3'- -UCUcAUGAGGCGGCCAuuAUUUGg----GG- -5' |
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| 27332 | 3' | -50.4 | NC_005857.1 | + | 22651 | 0.7 | 0.776923 |
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Target: 5'- uGGuGU-UUCCGCCGGUGAauAACgCCu -3' miRNA: 3'- -UCuCAuGAGGCGGCCAUUauUUGgGG- -5' |
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| 27332 | 3' | -50.4 | NC_005857.1 | + | 7240 | 0.77 | 0.38884 |
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Target: 5'- cGGGUACgcaUCCauGCCGGUGAUGcGCUCCa -3' miRNA: 3'- uCUCAUG---AGG--CGGCCAUUAUuUGGGG- -5' |
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| 27332 | 3' | -50.4 | NC_005857.1 | + | 2396 | 1.14 | 0.001509 |
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Target: 5'- cAGAGUACUCCGCCGGUAAUAAACCCCg -3' miRNA: 3'- -UCUCAUGAGGCGGCCAUUAUUUGGGG- -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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