miRNA: 3'- -AACUGCUAGAGAGCCGGCUGAUCCGG- -5'
miRNA: 3'- aaCUGCUA----GAGaGCCGGCUGAU------------CCGG- -5'
miRNA: 3'- -AACUGCU---AGAGAGCCGGcUGaUCCGG- -5'
miRNA: 3'- aaCUGCUAGag---AG-CCGGCUgauCCGG- -5'
miRNA: 3'- aaCUGCuAGaGaGCCGGCUGAU--CCGg -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 | |||||||
| 12173 | 5' | -55.8 | NC_003309.1 | + | 43340 | 1.1 | 0.000703 |
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Target: 5'- cUUGACGAUCUCUCGGCCGACUAGGCCg -3' miRNA: 3'- -AACUGCUAGAGAGCCGGCUGAUCCGG- -5' |
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| 12173 | 5' | -55.8 | NC_003309.1 | + | 37651 | 0.74 | 0.253375 |
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Target: 5'- -cGACGAUguucCUCgCGGCCGGCUGcgauaacgucccGGCCg -3' miRNA: 3'- aaCUGCUA----GAGaGCCGGCUGAU------------CCGG- -5' |
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| 12173 | 5' | -55.8 | NC_003309.1 | + | 50606 | 0.72 | 0.350485 |
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Target: 5'- cUUGACGAucuUCUCUUGGCCuGC-GGGUCc -3' miRNA: 3'- -AACUGCU---AGAGAGCCGGcUGaUCCGG- -5' |
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| 12173 | 5' | -55.8 | NC_003309.1 | + | 31692 | 0.67 | 0.609851 |
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Target: 5'- -cGACGAUCgugaaUCaGGCCGA---GGCCg -3' miRNA: 3'- aaCUGCUAGag---AG-CCGGCUgauCCGG- -5' |
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| 12173 | 5' | -55.8 | NC_003309.1 | + | 44447 | 0.66 | 0.664964 |
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Target: 5'- -cGACG-UCgCcCGGCCGACUGccGGCg -3' miRNA: 3'- aaCUGCuAGaGaGCCGGCUGAU--CCGg -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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