miRNA: 3'- aUGGCGa--AGCCG----CA-GCUCGAcCUCCU- -5'
miRNA: 3'- aUGGCGAAGCCGc----AGCUCga---CCUCCu -5'
miRNA: 3'- aUGGCGAAGcCGc------AGCUCGACC------------UCCU- -5'
miRNA: 3'- aUGGCGa---AGcCGCAGCUCGACCUCcu -5'
miRNA: 3'- -AUGGCGAAGCCGCAGCUCGACCUCCU- -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 | |||||||
| 22301 | 3' | -58.7 | NC_005045.1 | + | 32942 | 0.66 | 0.414035 |
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Target: 5'- cGCCGCcggUCGGCaacuGUcCGAGUUcGAGGAg -3' miRNA: 3'- aUGGCGa--AGCCG----CA-GCUCGAcCUCCU- -5' |
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| 22301 | 3' | -58.7 | NC_005045.1 | + | 19590 | 0.67 | 0.386474 |
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Target: 5'- aGCCGCUUCGGUaccccUCGGGauuccGGAGGc -3' miRNA: 3'- aUGGCGAAGCCGc----AGCUCga---CCUCCu -5' |
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| 22301 | 3' | -58.7 | NC_005045.1 | + | 14163 | 0.68 | 0.319126 |
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Target: 5'- gGCCGCUUCuGCaucuacaUCGAGCUGGgugaccacgccaAGGAa -3' miRNA: 3'- aUGGCGAAGcCGc------AGCUCGACC------------UCCU- -5' |
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| 22301 | 3' | -58.7 | NC_005045.1 | + | 31878 | 0.78 | 0.067262 |
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Target: 5'- cGCCGCaaggUCuGCGUCGAGCUGGAGc- -3' miRNA: 3'- aUGGCGa---AGcCGCAGCUCGACCUCcu -5' |
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| 22301 | 3' | -58.7 | NC_005045.1 | + | 6415 | 1.07 | 0.000453 |
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Target: 5'- aUACCGCUUCGGCGUCGAGCUGGAGGAc -3' miRNA: 3'- -AUGGCGAAGCCGCAGCUCGACCUCCU- -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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