miRNA: 3'- cuGCAGCuaaAGGA--GGCGGUCGCCGa -5'
miRNA: 3'- -CUGCaGCUaaa--GGAGGCGG---------------UCGCCGa -5'
miRNA: 3'- cUGCAGCUAaaGGa-GGCGg--UCGCCGA- -5'
miRNA: 3'- cUGCA-GCuaAAGGAGGCG--GUCGCCGa -5'
miRNA: 3'- -CUGCAGCUAAAGGAGGCGGUCGCCGA- -5'
Results 41 - 45 of 45 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 | |||||||
| 24739 | 5' | -56.8 | NC_005264.1 | + | 113248 | 0.71 | 0.627903 |
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Target: 5'- -cCGUCG---UCCUggUCGCCGGCGGCg -3' miRNA: 3'- cuGCAGCuaaAGGA--GGCGGUCGCCGa -5' |
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| 24739 | 5' | -56.8 | NC_005264.1 | + | 80993 | 0.72 | 0.551407 |
|
Target: 5'- cGACGcCGAcguggCCUCCGCCuugguggucgaagccAGCGGCg -3' miRNA: 3'- -CUGCaGCUaaa--GGAGGCGG---------------UCGCCGa -5' |
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| 24739 | 5' | -56.8 | NC_005264.1 | + | 128050 | 0.73 | 0.537576 |
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Target: 5'- cGCGUCGAUggCCgcCCGCaugAGCGGCUc -3' miRNA: 3'- cUGCAGCUAaaGGa-GGCGg--UCGCCGA- -5' |
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| 24739 | 5' | -56.8 | NC_005264.1 | + | 107604 | 0.75 | 0.425314 |
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Target: 5'- aGCGUaCGcgUUCUUCCGCuuCAGCGGCg -3' miRNA: 3'- cUGCA-GCuaAAGGAGGCG--GUCGCCGa -5' |
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| 24739 | 5' | -56.8 | NC_005264.1 | + | 145142 | 1.08 | 0.003182 |
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Target: 5'- uGACGUCGAUUUCCUCCGCCAGCGGCUg -3' miRNA: 3'- -CUGCAGCUAAAGGAGGCGGUCGCCGA- -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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