miRNA: 3'- -UCCC---UCCGGCgcCGGAGGGUUC--CCGC- -5'
miRNA: 3'- -UCCC-UCCG-GCGCCGG---AGGGUU-CCCGC- -5'
miRNA: 3'- -UCCCUCCg----GCGCCGGaGGGUUCCCgC- -5'
miRNA: 3'- uCCCUCCGGCGCCGGAGGG-------UUCCCgc -5'
miRNA: 3'- -UCCCUCCGGCGCCGGAGGGUUCCCGC- -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 | |||||||
| 27484 | 5' | -66 | NC_005872.1 | + | 20591 | 0.66 | 0.146383 |
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Target: 5'- gAGGGcuaAGGCUGa-GCCUCCUAGGgaGGUGg -3' miRNA: 3'- -UCCC---UCCGGCgcCGGAGGGUUC--CCGC- -5' |
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| 27484 | 5' | -66 | NC_005872.1 | + | 26674 | 0.72 | 0.046323 |
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Target: 5'- aAGGGcGGGCaCGUGGCUuuuUCCUAAgGGGCGc -3' miRNA: 3'- -UCCC-UCCG-GCGCCGG---AGGGUU-CCCGC- -5' |
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| 27484 | 5' | -66 | NC_005872.1 | + | 3266 | 0.75 | 0.023837 |
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Target: 5'- cGGGGGGGaaacgCGCGGCC-CCUAAGGGgGc -3' miRNA: 3'- -UCCCUCCg----GCGCCGGaGGGUUCCCgC- -5' |
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| 27484 | 5' | -66 | NC_005872.1 | + | 1328 | 0.87 | 0.002357 |
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Target: 5'- uGGGAGGCCGCGGCCUCCCucccgacAAGGGa- -3' miRNA: 3'- uCCCUCCGGCGCCGGAGGG-------UUCCCgc -5' |
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| 27484 | 5' | -66 | NC_005872.1 | + | 1376 | 1.07 | 5e-05 |
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Target: 5'- gAGGGAGGCCGCGGCCUCCCAAGGGCGu -3' miRNA: 3'- -UCCCUCCGGCGCCGGAGGGUUCCCGC- -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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