miRNA: 3'- gACG------UCGUCUAAGGCA-GAGCGUUGuu -5'
miRNA: 3'- gACGUCGUCuaAGGcaGAGCGUUGUU- -5'
miRNA: 3'- gACguCGUC--------------UAAGGCAGAg--CGUUGUU- -5'
miRNA: 3'- -GACGUCGUCUAAGGCAGAGCGUUGUU- -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 |
| Predicted miRNA align pattern | |||||||
| 28205 | 3' | -52.3 | NC_005891.1 | + | 28822 | 0.69 | 0.569262 |
|
Target: 5'- uUGUauuuugGGCGGGUUCCGUcCUCGUGGCu- -3' miRNA: 3'- gACG------UCGUCUAAGGCA-GAGCGUUGuu -5' |
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| 28205 | 3' | -52.3 | NC_005891.1 | + | 19798 | 0.67 | 0.686124 |
|
Target: 5'- aUGCGGCAGc-UCCaaUUCGCGGCGAg -3' miRNA: 3'- gACGUCGUCuaAGGcaGAGCGUUGUU- -5' |
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| 28205 | 3' | -52.3 | NC_005891.1 | + | 7477 | 0.66 | 0.750886 |
|
Target: 5'- uUGguGCAGcccaauacgcccgaAUUCCGUCUgaaGUAACAAu -3' miRNA: 3'- gACguCGUC--------------UAAGGCAGAg--CGUUGUU- -5' |
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| 28205 | 3' | -52.3 | NC_005891.1 | + | 27719 | 1.07 | 0.001381 |
|
Target: 5'- aCUGCAGCAGAUUCCGUCUCGCAACAAg -3' miRNA: 3'- -GACGUCGUCUAAGGCAGAGCGUUGUU- -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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