miRNA: 3'- -CGGCAcccgUGGGACuaGUUGGACUG- -5'
miRNA: 3'- -CGgCAC----CCGUGGGACUAGUUGga--CUg -5'
miRNA: 3'- cGGCa--CCCGUGGGACUA---GUUGGACUg -5'
miRNA: 3'- -CGGCACCCGUGgg-ACU--AGUUGGACUg -5'
miRNA: 3'- -CGGCACCCGUGGGACUAGUUGGACUG- -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 | |||||||
| 11394 | 3' | -56.5 | NC_003084.1 | + | 95684 | 0.66 | 0.827166 |
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Target: 5'- cGCCGUa---GCCCUGucCAACCUGGCc -3' miRNA: 3'- -CGGCAcccgUGGGACuaGUUGGACUG- -5' |
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| 11394 | 3' | -56.5 | NC_003084.1 | + | 83316 | 0.67 | 0.772363 |
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Target: 5'- gGCgGUGaugaGGCGCCCUGAUUAACaaaaGAa -3' miRNA: 3'- -CGgCAC----CCGUGGGACUAGUUGga--CUg -5' |
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| 11394 | 3' | -56.5 | NC_003084.1 | + | 67613 | 0.7 | 0.598503 |
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Target: 5'- aCUGaacGGGCACCUUGAUgggCGACCUGGa -3' miRNA: 3'- cGGCa--CCCGUGGGACUA---GUUGGACUg -5' |
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| 11394 | 3' | -56.5 | NC_003084.1 | + | 63749 | 0.75 | 0.314661 |
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Target: 5'- gGCCGUGGGCACagaUGGagUCAACUUGGa -3' miRNA: 3'- -CGGCACCCGUGgg-ACU--AGUUGGACUg -5' |
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| 11394 | 3' | -56.5 | NC_003084.1 | + | 81768 | 1.11 | 0.001278 |
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Target: 5'- cGCCGUGGGCACCCUGAUCAACCUGACc -3' miRNA: 3'- -CGGCACCCGUGGGACUAGUUGGACUG- -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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