miRNA: 3'- aGAG-GCUGaAGCCGCGCUU-GCAgaCG- -5'
miRNA: 3'- -AGAGG-CUgaAGCCGCGCU-----UGCa-GA-CG- -5'
miRNA: 3'- -AGAGg-----CUGAAGCCGCGC-------UUGCAGA------CG- -5'
miRNA: 3'- -AGAGgCUGAaGCCGCGCuUGCaGaCG- -5'
miRNA: 3'- -AGAGGCUGAAGCCGCGCUUGCAGACG- -5'
Results 21 - 25 of 25 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 | |||||||
| 22560 | 3' | -54.5 | NC_005091.1 | + | 17077 | 0.71 | 0.531307 |
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Target: 5'- gCUCuCGACcUCGGCGCGAAgUGUa-GCa -3' miRNA: 3'- aGAG-GCUGaAGCCGCGCUU-GCAgaCG- -5' |
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| 22560 | 3' | -54.5 | NC_005091.1 | + | 36976 | 0.71 | 0.520817 |
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Target: 5'- uUCUCCuGAgaUCGGCGCGAugaugGCGcgCUcGCg -3' miRNA: 3'- -AGAGG-CUgaAGCCGCGCU-----UGCa-GA-CG- -5' |
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| 22560 | 3' | -54.5 | NC_005091.1 | + | 36085 | 0.71 | 0.49906 |
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Target: 5'- uUCUCgcgcagGACUUCGGCGCGcgccuucAGCGUCUccgggaGCa -3' miRNA: 3'- -AGAGg-----CUGAAGCCGCGC-------UUGCAGA------CG- -5' |
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| 22560 | 3' | -54.5 | NC_005091.1 | + | 27333 | 0.71 | 0.479731 |
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Target: 5'- aUCUCgGACUgCGGCGCG-ACGcCaGCc -3' miRNA: 3'- -AGAGgCUGAaGCCGCGCuUGCaGaCG- -5' |
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| 22560 | 3' | -54.5 | NC_005091.1 | + | 5541 | 1.13 | 0.000781 |
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Target: 5'- uUCUCCGACUUCGGCGCGAACGUCUGCa -3' miRNA: 3'- -AGAGGCUGAAGCCGCGCUUGCAGACG- -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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