miRNA: 3'- gUGCCCu--UUUGGgCUCGa----UAGAa-----GCG- -5'
miRNA: 3'- gUGCCCU-UUUGGGCU-CGAua-GAAGCg -5'
miRNA: 3'- gUGCCCUUU--UGGGCuCGaua---GAAGCG- -5'
miRNA: 3'- -GUGCCCUUUUGGGCUCGAUAGAAGCG- -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 | |||||||
| 7608 | 5' | -50.6 | NC_001963.1 | + | 2423 | 0.66 | 0.276878 |
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Target: 5'- uGCGGGuucGGGCCgGGGCguggcAUCUgaggggCGCg -3' miRNA: 3'- gUGCCCu--UUUGGgCUCGa----UAGAa-----GCG- -5' |
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| 7608 | 5' | -50.6 | NC_001963.1 | + | 3834 | 0.68 | 0.214322 |
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Target: 5'- gGCGGGGuGAACCUGAuGCUcgaCUUCGa -3' miRNA: 3'- gUGCCCU-UUUGGGCU-CGAua-GAAGCg -5' |
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| 7608 | 5' | -50.6 | NC_001963.1 | + | 4776 | 0.72 | 0.105071 |
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Target: 5'- aGCGGGAAAccACCCGcGCccauggUUUCGCa -3' miRNA: 3'- gUGCCCUUU--UGGGCuCGaua---GAAGCG- -5' |
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| 7608 | 5' | -50.6 | NC_001963.1 | + | 3665 | 1.13 | 5.3e-05 |
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Target: 5'- aCACGGGAAAACCCGAGCUAUCUUCGCu -3' miRNA: 3'- -GUGCCCUUUUGGGCUCGAUAGAAGCG- -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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