miRNA: 3'- ucaUCAauUAGUUUg------UAUGAGUCUCG- -5'
miRNA: 3'- -UCAUCaAUUAGUUUGU---AUGag---UCUCG- -5'
miRNA: 3'- uCAUC-AAUUAG-UUUGUaUGAGUCUCG- -5'
miRNA: 3'- -UCAUCAAUUAGUUUGUAUGAGUCUCG- -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 | |||||||
| 32324 | 3' | -40.8 | NC_007024.1 | + | 756 | 0.66 | 0.999998 |
|
Target: 5'- --aAGUc-AUCGAAgcgcugaAUGCUCAGAGCg -3' miRNA: 3'- ucaUCAauUAGUUUg------UAUGAGUCUCG- -5' |
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| 32324 | 3' | -40.8 | NC_007024.1 | + | 6372 | 0.68 | 0.99994 |
|
Target: 5'- aGGUGGcUGAUCAAGCAccaUGCcagaaAGGGCc -3' miRNA: 3'- -UCAUCaAUUAGUUUGU---AUGag---UCUCG- -5' |
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| 32324 | 3' | -40.8 | NC_007024.1 | + | 26281 | 0.83 | 0.741036 |
|
Target: 5'- cGUGGcUUAAUCuGAGCGcACUCAGAGCg -3' miRNA: 3'- uCAUC-AAUUAG-UUUGUaUGAGUCUCG- -5' |
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| 32324 | 3' | -40.8 | NC_007024.1 | + | 37413 | 1.17 | 0.012843 |
|
Target: 5'- aAGUAGUUAAUCAAACAUACUCAGAGCg -3' miRNA: 3'- -UCAUCAAUUAGUUUGUAUGAGUCUCG- -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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