miRNA: 3'- ggGAGGCGCGuAGAGGCa-----CGAUUCUu -5'
miRNA: 3'- gGGAGGCGCG--UAGAG--------GCA-CGAUUCUU- -5'
miRNA: 3'- gGGAGGCgC-GUAGaGGCACGAUUCUu -5'
miRNA: 3'- -GGGAGGCGCGUAGAGGCACGAUUCUU- -5'
Results 1 - 4 of 4 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 | |||||||
| 12564 | 3' | -55.5 | NC_003345.1 | + | 68291 | 0.66 | 0.7834 |
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Target: 5'- -gCUCCGUGCuUCUCUGaacgacGCUGAGGu -3' miRNA: 3'- ggGAGGCGCGuAGAGGCa-----CGAUUCUu -5' |
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| 12564 | 3' | -55.5 | NC_003345.1 | + | 14315 | 0.68 | 0.647953 |
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Target: 5'- gCCUCCGCGUacAUCUCgcggagaaCGUcGUUGAGAAu -3' miRNA: 3'- gGGAGGCGCG--UAGAG--------GCA-CGAUUCUU- -5' |
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| 12564 | 3' | -55.5 | NC_003345.1 | + | 8650 | 0.7 | 0.551288 |
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Target: 5'- uUCUCCGgGuCGUCgCCGUGUUGGGAc -3' miRNA: 3'- gGGAGGCgC-GUAGaGGCACGAUUCUu -5' |
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| 12564 | 3' | -55.5 | NC_003345.1 | + | 49141 | 1.08 | 0.001624 |
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Target: 5'- cCCCUCCGCGCAUCUCCGUGCUAAGAAu -3' miRNA: 3'- -GGGAGGCGCGUAGAGGCACGAUUCUU- -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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