miRNA: 3'- cACUcAAGUAGU---AUGUGUuaUUUGGu -5'
miRNA: 3'- cACUCAAG----UAGUa-UGUG-UUAUUUGGU- -5'
miRNA: 3'- caCUCAAGUAGUAUGUGUUAUUUGgu -5'
miRNA: 3'- -CACUCAAGUAGUAUGUGUUAUUUGGU- -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 | |||||||
| 21128 | 5' | -41.6 | NC_004775.1 | + | 6651 | 0.66 | 0.999867 |
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Target: 5'- uUGAaUUCGUCAcggUACGCAcgGAACUg -3' miRNA: 3'- cACUcAAGUAGU---AUGUGUuaUUUGGu -5' |
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| 21128 | 5' | -41.6 | NC_004775.1 | + | 36601 | 0.67 | 0.999457 |
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Target: 5'- aUGAGUUUgaagAUUAcgGCACgAAUGAACCAg -3' miRNA: 3'- cACUCAAG----UAGUa-UGUG-UUAUUUGGU- -5' |
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| 21128 | 5' | -41.6 | NC_004775.1 | + | 24766 | 0.86 | 0.416896 |
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Target: 5'- -gGGGUUCGUUAUGCACAGUAAACg- -3' miRNA: 3'- caCUCAAGUAGUAUGUGUUAUUUGgu -5' |
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| 21128 | 5' | -41.6 | NC_004775.1 | + | 24796 | 1.11 | 0.015771 |
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Target: 5'- gGUGAGUUCAUCAUACACAAUAAACCAc -3' miRNA: 3'- -CACUCAAGUAGUAUGUGUUAUUUGGU- -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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