miRNA: 3'- cGACGGCAACAUCggCGgCGUC----GGAU- -5'
miRNA: 3'- -CGACGGCA---------ACAUcGGCGG---CGUCGGau -5'
miRNA: 3'- -CGACGGCaacauCGGCGGCGUCGGau -5'
miRNA: 3'- cgACGGCa---ACa---UCGGCGgCGUCGGau -5'
miRNA: 3'- -CGACGGCAACAUCGGCGGCGUCGGAU- -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 | |||||||
| 31933 | 3' | -59.1 | NC_006940.1 | + | 3969 | 0.66 | 0.400839 |
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Target: 5'- aUUGCCGUUGUGGuaGCgGCGGgauaUCUAa -3' miRNA: 3'- cGACGGCAACAUCggCGgCGUC----GGAU- -5' |
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| 31933 | 3' | -59.1 | NC_006940.1 | + | 2734 | 0.7 | 0.219204 |
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Target: 5'- gGCUGCCGUuaugcuuacUGUA-CCGCCugaGUAGCCa- -3' miRNA: 3'- -CGACGGCA---------ACAUcGGCGG---CGUCGGau -5' |
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| 31933 | 3' | -59.1 | NC_006940.1 | + | 37030 | 0.71 | 0.176467 |
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Target: 5'- uGCUGCUGcu---GCUGCCGUAGCCg- -3' miRNA: 3'- -CGACGGCaacauCGGCGGCGUCGGau -5' |
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| 31933 | 3' | -59.1 | NC_006940.1 | + | 3960 | 0.73 | 0.133573 |
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Target: 5'- -gUGCCGguagUGgugcAGCCGCgGCAGCCg- -3' miRNA: 3'- cgACGGCa---ACa---UCGGCGgCGUCGGau -5' |
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| 31933 | 3' | -59.1 | NC_006940.1 | + | 38855 | 1.08 | 0.00027 |
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Target: 5'- gGCUGCCGUUGUAGCCGCCGCAGCCUAu -3' miRNA: 3'- -CGACGGCAACAUCGGCGGCGUCGGAU- -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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