miRNA: 3'- -GAGUGACUGUUGC---AGUUCCcGa--UAGa -5'
miRNA: 3'- gAGUGACUGuugcAGUUCCCGa--UAGa -5'
miRNA: 3'- -GAG---UGACUGUUGCAguuCCCGAUAGa -5'
miRNA: 3'- -GAGUGACUGUUGCAGUUCCCGAUAGA- -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 | |||||||
| 31902 | 3' | -50 | NC_006938.1 | + | 45894 | 0.69 | 0.862754 |
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Target: 5'- cCUCGCUGACGGCGgcuUCGAGGuCcugAUCg -3' miRNA: 3'- -GAGUGACUGUUGC---AGUUCCcGa--UAGa -5' |
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| 31902 | 3' | -50 | NC_006938.1 | + | 23889 | 0.7 | 0.787905 |
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Target: 5'- aUCACUGGCu---UCAAGGGCgugAUCg -3' miRNA: 3'- gAGUGACUGuugcAGUUCCCGa--UAGa -5' |
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| 31902 | 3' | -50 | NC_006938.1 | + | 63077 | 0.75 | 0.533012 |
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Target: 5'- cCUCccuGCUGGCAACGU---GGGCUGUCg -3' miRNA: 3'- -GAG---UGACUGUUGCAguuCCCGAUAGa -5' |
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| 31902 | 3' | -50 | NC_006938.1 | + | 57210 | 1.08 | 0.00462 |
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Target: 5'- gCUCACUGACAACGUCAAGGGCUAUCUc -3' miRNA: 3'- -GAGUGACUGUUGCAGUUCCCGAUAGA- -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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