miRNA: 3'- ugCAGAGGc-UCUAGAAAUGU-GCAGCg -5'
miRNA: 3'- ugcaGAGGCUCUAGA--AAUGugCAGcg -5'
miRNA: 3'- -UGCAGAGGCUCUAGAAAUGUGCAGCG- -5'
miRNA: 3'- -UGCAGAGGcUCUaGAAa---UG-------------UGCAGCG- -5'
miRNA: 3'- uGCAGAGGCUC---UAGAAA--UGUGCaGCG- -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 |
| Predicted miRNA align pattern | |||||||
| 28395 | 3' | -49.4 | NC_005946.1 | + | 18645 | 0.73 | 0.865131 |
|
Target: 5'- -aGUCUCCcaGGAUCUUUACAuUGUCGa -3' miRNA: 3'- ugCAGAGGc-UCUAGAAAUGU-GCAGCg -5' |
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| 28395 | 3' | -49.4 | NC_005946.1 | + | 50064 | 0.68 | 0.984782 |
|
Target: 5'- ---cCUCUGGGAUCUggUUGCugGUCa- -3' miRNA: 3'- ugcaGAGGCUCUAGA--AAUGugCAGcg -5' |
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| 28395 | 3' | -49.4 | NC_005946.1 | + | 57352 | 1.13 | 0.005194 |
|
Target: 5'- aACGUCUCCGAGAUCUUUACACGUCGCg -3' miRNA: 3'- -UGCAGAGGCUCUAGAAAUGUGCAGCG- -5' |
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| 28395 | 3' | -49.4 | NC_005946.1 | + | 59833 | 0.67 | 0.992057 |
|
Target: 5'- aGCGUCUCCuGGAgCUUgacgGCcgugguacccuugACGUCGUa -3' miRNA: 3'- -UGCAGAGGcUCUaGAAa---UG-------------UGCAGCG- -5' |
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| 28395 | 3' | -49.4 | NC_005946.1 | + | 67785 | 0.71 | 0.926606 |
|
Target: 5'- uCGUCUCCGGGccuGUCUUUggGCAUGgCGUu -3' miRNA: 3'- uGCAGAGGCUC---UAGAAA--UGUGCaGCG- -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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