miRNA: 3'- gGACCCUuuucUGG---GCGUUACUGGcu -5'
miRNA: 3'- -GGACCCU-UUUCUG------------GGCGUUaCUGGCu -5'
miRNA: 3'- -GGACCCUUu---UCUGGG----CGUUaCUGGCu -5'
miRNA: 3'- -GGa--CCCUu------UUCUGGGCGuuaCUGGcu -5'
miRNA: 3'- -GGACCCUUUUCUGGGCGUUACUGGCU- -5'
Results 21 - 25 of 25 are showing below:
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| ID | Location | Perfect MFE.* | RefSeq Acc. |
strand
|
Start Position | R_P_ratio# | P value |
| Predicted miRNA align pattern | |||||||
| 2647 | 3' | -51.9 | NC_001491.2 | + | 84405 | 0.66 | 0.984411 |
|
Target: 5'- aCUGGGAcgcaACCacaCGCGAUGACCu- -3' miRNA: 3'- gGACCCUuuucUGG---GCGUUACUGGcu -5' |
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| 2647 | 3' | -51.9 | NC_001491.2 | + | 61429 | 0.66 | 0.986172 |
|
Target: 5'- uCCUGGGGuAGGGACguuacacgacugCUGCGA-GACCGc -3' miRNA: 3'- -GGACCCU-UUUCUG------------GGCGUUaCUGGCu -5' |
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| 2647 | 3' | -51.9 | NC_001491.2 | + | 64719 | 0.66 | 0.984411 |
|
Target: 5'- aUCUGGGGGcuccAGGCCCaacaGCAA-GGCCGu -3' miRNA: 3'- -GGACCCUUu---UCUGGG----CGUUaCUGGCu -5' |
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| 2647 | 3' | -51.9 | NC_001491.2 | + | 31203 | 0.66 | 0.984411 |
|
Target: 5'- cCCgagGGGGuggcuccGAGGCCCGCuucGACCu- -3' miRNA: 3'- -GGa--CCCUu------UUCUGGGCGuuaCUGGcu -5' |
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| 2647 | 3' | -51.9 | NC_001491.2 | + | 111972 | 1.12 | 0.004823 |
|
Target: 5'- aCCUGGGAAAAGACCCGCAAUGACCGAa -3' miRNA: 3'- -GGACCCUUUUCUGGGCGUUACUGGCU- -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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