miRNA: 3'- -UG-GUCGGaGGAGaAGG-------UGUCGG-CUCC- -5'
miRNA: 3'- -UG-GUCGGAGGAGAA-GGUGuCGGCUcc -5'
miRNA: 3'- -UGGUCGGaggaGAAGGUGUCGGCUcc -5'
miRNA: 3'- uGGUCGGAGGAGAAGGUgUCgg------CUCc -5'
miRNA: 3'- -UGGUCGGAGGAGAAGGUGUCGGCUCC- -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 | |||||||
| 22454 | 5' | -58.1 | NC_005062.1 | + | 9614 | 0.66 | 0.174457 |
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Target: 5'- cACgCAGCCaCCUC-UCCacucguaGCAGCCuGGGGu -3' miRNA: 3'- -UG-GUCGGaGGAGaAGG-------UGUCGG-CUCC- -5' |
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| 22454 | 5' | -58.1 | NC_005062.1 | + | 9088 | 0.68 | 0.121085 |
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Target: 5'- aGCuCGGCUUCCUUUUgCCAC-GCCGAa- -3' miRNA: 3'- -UG-GUCGGAGGAGAA-GGUGuCGGCUcc -5' |
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| 22454 | 5' | -58.1 | NC_005062.1 | + | 6785 | 0.72 | 0.058306 |
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Target: 5'- cACCGGCCaug-CUUCCAUAGCCGAc- -3' miRNA: 3'- -UGGUCGGaggaGAAGGUGUCGGCUcc -5' |
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| 22454 | 5' | -58.1 | NC_005062.1 | + | 7718 | 0.72 | 0.056454 |
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Target: 5'- uUCAGCCUCCUCUUCCAgAGaucaccaaGAGu -3' miRNA: 3'- uGGUCGGAGGAGAAGGUgUCgg------CUCc -5' |
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| 22454 | 5' | -58.1 | NC_005062.1 | + | 7930 | 1.09 | 4.3e-05 |
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Target: 5'- gACCAGCCUCCUCUUCCACAGCCGAGGu -3' miRNA: 3'- -UGGUCGGAGGAGAAGGUGUCGGCUCC- -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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