miRNA: 3'- ccuaaaAAUGGGUAC-GAGUGGCaauu -5'
miRNA: 3'- -CCUAAAAAUGGGU-------ACGAg---UGGCAauu -5'
miRNA: 3'- ccuAAAAAUGGGuACGAGUGG-CAAuu -5'
miRNA: 3'- -CCUAAAAAUGGGUACGAGUGGCAAUU- -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 | |||||||
| 26244 | 5' | -45 | NC_005344.1 | + | 552 | 0.67 | 0.987405 |
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Target: 5'- -----aUUGCCCAUGaCUUACCGc--- -3' miRNA: 3'- ccuaaaAAUGGGUAC-GAGUGGCaauu -5' |
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| 26244 | 5' | -45 | NC_005344.1 | + | 15768 | 0.67 | 0.985254 |
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Target: 5'- uGGGUUUUUACCCGucaauguUGUUaaguGCCGUg-- -3' miRNA: 3'- -CCUAAAAAUGGGU-------ACGAg---UGGCAauu -5' |
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| 26244 | 5' | -45 | NC_005344.1 | + | 35226 | 0.69 | 0.956412 |
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Target: 5'- --uUUUUUACCUuUGCUCACCaGUUc- -3' miRNA: 3'- ccuAAAAAUGGGuACGAGUGG-CAAuu -5' |
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| 26244 | 5' | -45 | NC_005344.1 | + | 17972 | 1.11 | 0.005685 |
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Target: 5'- cGGAUUUUUACCCAUGCUCACCGUUAAg -3' miRNA: 3'- -CCUAAAAAUGGGUACGAGUGGCAAUU- -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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