miRNA: 3'- -UCgUCGGU--AAGCGU----UUCUGUCG-GGUG- -5'
miRNA: 3'- -UCGUCGGuaaGCgUUUCUGUCgGGUg -5'
miRNA: 3'- -UCgUCGGUAAGCGUUUC-UGU---------------CGGGUG- -5'
miRNA: 3'- -UCgu-CGGUAAGC-GUuUCUGUCGGGUg -5'
Results 21 - 24 of 24 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 | |||||||
| 17485 | 3' | -53.9 | NC_004456.1 | + | 8648 | 0.68 | 0.520039 |
|
Target: 5'- uAGgGGCCGguUUUGCAaaccAAGACGGCaCCAUu -3' miRNA: 3'- -UCgUCGGU--AAGCGU----UUCUGUCG-GGUG- -5' |
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| 17485 | 3' | -53.9 | NC_004456.1 | + | 8396 | 0.67 | 0.599252 |
|
Target: 5'- aGGCAGCC---UGgGAAGACAGgCCGg -3' miRNA: 3'- -UCGUCGGuaaGCgUUUCUGUCgGGUg -5' |
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| 17485 | 3' | -53.9 | NC_004456.1 | + | 3413 | 0.69 | 0.480879 |
|
Target: 5'- cAGgAGCCAUUUGCGGAGuGCAuuugcuucuuugcuuGUCCACu -3' miRNA: 3'- -UCgUCGGUAAGCGUUUC-UGU---------------CGGGUG- -5' |
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| 17485 | 3' | -53.9 | NC_004456.1 | + | 1237 | 0.66 | 0.656924 |
|
Target: 5'- uGGaauGCUAUUCGaCAuAGAUGGCCCGg -3' miRNA: 3'- -UCgu-CGGUAAGC-GUuUCUGUCGGGUg -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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