miRNA: 3'- uAGGCCGa------GACg-CUGCCa-GuCGUACG- -5'
miRNA: 3'- -UAGGCCGagACGcuGcCAGUCGUACG- -5'
miRNA: 3'- -UAGGCCG-AGACGcUGCCAGUCGua---CG- -5'
miRNA: 3'- uagGCCGAGACG-CUGC------------CAGUCGUaCG- -5'
miRNA: 3'- -UAGGCCGAGACGCUGCCAGUCGUACG- -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 | |||||||
| 27345 | 3' | -57.6 | NC_005857.1 | + | 41372 | 0.66 | 0.539404 |
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Target: 5'- uUCUGGCggauucgCUGgaGACGGcgCuGCGUGCa -3' miRNA: 3'- uAGGCCGa------GACg-CUGCCa-GuCGUACG- -5' |
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| 27345 | 3' | -57.6 | NC_005857.1 | + | 15440 | 0.67 | 0.507732 |
|
Target: 5'- cAUCCGGC--UGCu-CcGUCGGCGUGCg -3' miRNA: 3'- -UAGGCCGagACGcuGcCAGUCGUACG- -5' |
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| 27345 | 3' | -57.6 | NC_005857.1 | + | 42367 | 0.68 | 0.408794 |
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Target: 5'- cAUCUGGCuUCUGCuGCGGUUAGUuccucGCc -3' miRNA: 3'- -UAGGCCG-AGACGcUGCCAGUCGua---CG- -5' |
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| 27345 | 3' | -57.6 | NC_005857.1 | + | 21926 | 0.71 | 0.299763 |
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Target: 5'- --gCGGCUCUGCaGACGcugcagaauaccGUCAGCA-GCa -3' miRNA: 3'- uagGCCGAGACG-CUGC------------CAGUCGUaCG- -5' |
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| 27345 | 3' | -57.6 | NC_005857.1 | + | 18730 | 1.1 | 0.000402 |
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Target: 5'- aAUCCGGCUCUGCGACGGUCAGCAUGCg -3' miRNA: 3'- -UAGGCCGAGACGCUGCCAGUCGUACG- -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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