miRNA: 3'- uUGCCAAGUCuaGG---UCGUCCCa----CGgu -5'
miRNA: 3'- uuGCCAAGUcUAGGUCGUcCCaCGGU- -5'
miRNA: 3'- -UugCC-AAGUCU------------AGGUCG---UCCCACG-GU- -5'
miRNA: 3'- -UUGCCAAGUCUAGGUCGUCCCACGGU- -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 | |||||||
| 12731 | 3' | -56.5 | NC_003356.1 | + | 35766 | 0.66 | 0.50339 |
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Target: 5'- uACGGUUCAGggCUggcGGCAGGGcagugGCg- -3' miRNA: 3'- uUGCCAAGUCuaGG---UCGUCCCa----CGgu -5' |
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| 12731 | 3' | -56.5 | NC_003356.1 | + | 17190 | 0.68 | 0.392708 |
|
Target: 5'- -cUGGUUCAaAUCCAGCAaGG-GCCAc -3' miRNA: 3'- uuGCCAAGUcUAGGUCGUcCCaCGGU- -5' |
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| 12731 | 3' | -56.5 | NC_003356.1 | + | 24810 | 0.68 | 0.383449 |
|
Target: 5'- aAugGGaUUCAGAccgacaaguccgUCCAGCgucAGGGUGCgCAc -3' miRNA: 3'- -UugCC-AAGUCU------------AGGUCG---UCCCACG-GU- -5' |
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| 12731 | 3' | -56.5 | NC_003356.1 | + | 29013 | 1.06 | 0.000749 |
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Target: 5'- uAACGGUUCAGAUCCAGCAGGGUGCCAc -3' miRNA: 3'- -UUGCCAAGUCUAGGUCGUCCCACGGU- -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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