miRNA: 3'- uuUCUGAGUUUGucggUGACAAUUCG- -5'
miRNA: 3'- uUUCugAGU-------------UUGUCGGUGACAAUU-CG- -5'
miRNA: 3'- -UUUCUGAGUUu--GUCGgugaCAAUUCG- -5'
miRNA: 3'- -UUUCUGAGUUUGUCGGUGACAAUUCG- -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 | |||||||
| 24802 | 5' | -45.5 | NC_005282.1 | + | 30596 | 0.66 | 0.999346 |
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Target: 5'- -uGGACUUAAAU----GCUGUUAAGCa -3' miRNA: 3'- uuUCUGAGUUUGucggUGACAAUUCG- -5' |
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| 24802 | 5' | -45.5 | NC_005282.1 | + | 19525 | 0.67 | 0.997623 |
|
Target: 5'- cAAGugUUAccucagaugcggcAACAGUUACUGUUAAuGCa -3' miRNA: 3'- uUUCugAGU-------------UUGUCGGUGACAAUU-CG- -5' |
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| 24802 | 5' | -45.5 | NC_005282.1 | + | 16335 | 0.68 | 0.996614 |
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Target: 5'- uAAGGACUCAAucuCAGCa---GUUGAGUa -3' miRNA: 3'- -UUUCUGAGUUu--GUCGgugaCAAUUCG- -5' |
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| 24802 | 5' | -45.5 | NC_005282.1 | + | 46284 | 1.1 | 0.011958 |
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Target: 5'- cAAAGACUCAAACAGCCACUGUUAAGCc -3' miRNA: 3'- -UUUCUGAGUUUGUCGGUGACAAUUCG- -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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