miRNA: 3'- -CGUUC------AACGUUGCgucCCACCAUAac -5'
miRNA: 3'- -CGUUCaACGU---UG-CGUCCCAcCAUaAC- -5'
miRNA: 3'- cGUUCAACGUUGCGU-----CCCaCCAuaac -5'
miRNA: 3'- -CGUUCAACGUUGCGUCCCACCAUAAC- -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 | |||||||
| 27994 | 3' | -49.1 | NC_005886.2 | + | 12908 | 0.67 | 0.921858 |
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Target: 5'- gGCAAGcagcacUUGCGGCGaucGGUGGUGUg- -3' miRNA: 3'- -CGUUC------AACGUUGCgucCCACCAUAac -5' |
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| 27994 | 3' | -49.1 | NC_005886.2 | + | 31886 | 0.68 | 0.886232 |
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Target: 5'- aGCAAGgUGCAucgGCuGCAGGGUuGUAcUGa -3' miRNA: 3'- -CGUUCaACGU---UG-CGUCCCAcCAUaAC- -5' |
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| 27994 | 3' | -49.1 | NC_005886.2 | + | 44183 | 0.7 | 0.783601 |
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Target: 5'- aCGAGUUGCGGCGCAgcgacGGG-GGUc--- -3' miRNA: 3'- cGUUCAACGUUGCGU-----CCCaCCAuaac -5' |
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| 27994 | 3' | -49.1 | NC_005886.2 | + | 44067 | 1.11 | 0.00244 |
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Target: 5'- aGCAAGUUGCAACGCAGGGUGGUAUUGc -3' miRNA: 3'- -CGUUCAACGUUGCGUCCCACCAUAAC- -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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