miRNA: 3'- aCUAAAa-AGUAUUGC-UGAGGCAAaac -5'
miRNA: 3'- -ACUAAA----AAGUAU-----UGCUGAGGCaaaac -5'
miRNA: 3'- -ACUa---AAAAGUAUuGCUGAGGCAAaac -5'
miRNA: 3'- -ACUAaa------AAGUAUUGC-------UGAGGCAAAAC- -5'
miRNA: 3'- -ACUAAAAAGUAUUGCUGAGGCAAAAC- -5'
Results 1 - 5 of 5 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 | |||||||
| 23531 | 3' | -39.5 | NC_005260.1 | + | 6147 | 0.69 | 1 |
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Target: 5'- gGAUUUcgUUAUAACGuACUUCGUUg-- -3' miRNA: 3'- aCUAAAa-AGUAUUGC-UGAGGCAAaac -5' |
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| 23531 | 3' | -39.5 | NC_005260.1 | + | 97185 | 0.67 | 1 |
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Target: 5'- uUGAUUUgauaUUCGUAuuauaGCGACUCUGg---- -3' miRNA: 3'- -ACUAAA----AAGUAU-----UGCUGAGGCaaaac -5' |
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| 23531 | 3' | -39.5 | NC_005260.1 | + | 148617 | 0.67 | 1 |
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Target: 5'- aUGAgcaaUUUUCAUAcCGAUUCUGUUc-- -3' miRNA: 3'- -ACUa---AAAAGUAUuGCUGAGGCAAaac -5' |
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| 23531 | 3' | -39.5 | NC_005260.1 | + | 192102 | 0.71 | 1 |
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Target: 5'- aUGAUagaacaagUUUAUGACGgacaacaGCUCCGUUUUGu -3' miRNA: 3'- -ACUAaa------AAGUAUUGC-------UGAGGCAAAAC- -5' |
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| 23531 | 3' | -39.5 | NC_005260.1 | + | 52347 | 1.11 | 0.153366 |
|
Target: 5'- uUGAUUUUUCAUAACGACUCCGUUUUGu -3' miRNA: 3'- -ACUAAAAAGUAUUGCUGAGGCAAAAC- -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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