miRNA: 3'- cuUUUCGGgUCaaGUAaCGGa----CCCGG- -5'
miRNA: 3'- cuuUUCGGGUCaa-GUA------ACGG----ACCCGG- -5'
miRNA: 3'- cUUUUCGGGucaaGUa-ACGGaCCCGG- -5'
miRNA: 3'- -CUUUUCGGGUCAAGUAACGGACCCGG- -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 | |||||||
| 8873 | 3' | -52 | NC_002484.1 | + | 18248 | 0.66 | 0.849999 |
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Target: 5'- -cAGGGCCgGGaaCAUcGCCggcaaGGGCCa -3' miRNA: 3'- cuUUUCGGgUCaaGUAaCGGa----CCCGG- -5' |
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| 8873 | 3' | -52 | NC_002484.1 | + | 7157 | 0.66 | 0.849999 |
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Target: 5'- --cGGGCCUAGcugCGUguuaggUGCCcuugUGGGCCa -3' miRNA: 3'- cuuUUCGGGUCaa-GUA------ACGG----ACCCGG- -5' |
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| 8873 | 3' | -52 | NC_002484.1 | + | 53392 | 0.68 | 0.74057 |
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Target: 5'- aAAAAGCCCcgg-CAgaUGCCaGGGCCu -3' miRNA: 3'- cUUUUCGGGucaaGUa-ACGGaCCCGG- -5' |
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| 8873 | 3' | -52 | NC_002484.1 | + | 54258 | 1.12 | 0.001085 |
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Target: 5'- aGAAAAGCCCAGUUCAUUGCCUGGGCCu -3' miRNA: 3'- -CUUUUCGGGUCAAGUAACGGACCCGG- -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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