miRNA: 3'- -UGUGUGCCUCGUGGGUCGAGACCCGU- -5'
miRNA: 3'- uGUgUGCCUCGUGGg------UCGa-GACCCGu -5'
miRNA: 3'- ugUG-UGCCUCGugGGUCGAga-----CCCGU- -5'
miRNA: 3'- -UGUGU-------------GCCUCGUGGGUc--------GAGACCC-GU- -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 | |||||||
| 30269 | 5' | -59.9 | NC_006296.2 | + | 4579 | 1.08 | 0.000058 |
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Target: 5'- aACACACGGAGCACCCAGCUCUGGGCAg -3' miRNA: 3'- -UGUGUGCCUCGUGGGUCGAGACCCGU- -5' |
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| 30269 | 5' | -59.9 | NC_006296.2 | + | 5297 | 0.69 | 0.104801 |
|
Target: 5'- cCAgGCGGAGCACCaagggcaAGCcaCUGGGUc -3' miRNA: 3'- uGUgUGCCUCGUGGg------UCGa-GACCCGu -5' |
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| 30269 | 5' | -59.9 | NC_006296.2 | + | 8186 | 0.67 | 0.129557 |
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Target: 5'- -uGCgACGGGGCugUCAGCUaggcagaGGGCAg -3' miRNA: 3'- ugUG-UGCCUCGugGGUCGAga-----CCCGU- -5' |
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| 30269 | 5' | -59.9 | NC_006296.2 | + | 13066 | 0.67 | 0.133107 |
|
Target: 5'- aGCACAuagacucagggauCGGAGUACCCAaguuaaguaCUCUGGGaCAu -3' miRNA: 3'- -UGUGU-------------GCCUCGUGGGUc--------GAGACCC-GU- -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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