miRNA: 3'- -UGACGUGGUGgGGGaaauaGG--UGCau -5'
miRNA: 3'- ugaCGUGGUGgGGGaaAUa--GGUGCau -5'
miRNA: 3'- ugAC-GUGGUGGGGGAAaua-GGUGcau -5'
miRNA: 3'- uGACGUGGUGG---GGGa--AAUAGG-UGCAU- -5'
miRNA: 3'- -UGACGUGGUGGGGGAAAUAGGUGCAU- -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 | |||||||
| 12477 | 5' | -54.3 | NC_003324.1 | + | 50508 | 0.66 | 0.759708 |
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Target: 5'- aGCUGCACCACgCCCagcg-CCuuGCGg- -3' miRNA: 3'- -UGACGUGGUGgGGGaaauaGG--UGCau -5' |
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| 12477 | 5' | -54.3 | NC_003324.1 | + | 40507 | 0.66 | 0.738558 |
|
Target: 5'- --cGCACCACgCCCgaUGgagCCACGa- -3' miRNA: 3'- ugaCGUGGUGgGGGaaAUa--GGUGCau -5' |
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| 12477 | 5' | -54.3 | NC_003324.1 | + | 44896 | 0.66 | 0.738558 |
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Target: 5'- -aUGaCGCCGCCCCCUUcuccCCGCa-- -3' miRNA: 3'- ugAC-GUGGUGGGGGAAaua-GGUGcau -5' |
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| 12477 | 5' | -54.3 | NC_003324.1 | + | 31178 | 0.72 | 0.406259 |
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Target: 5'- cCUGCGCCAUCaggCCCgggUUAUCCgACGUGa -3' miRNA: 3'- uGACGUGGUGG---GGGa--AAUAGG-UGCAU- -5' |
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| 12477 | 5' | -54.3 | NC_003324.1 | + | 47126 | 1.06 | 0.001637 |
|
Target: 5'- gACUGCACCACCCCCUUUAUCCACGUAu -3' miRNA: 3'- -UGACGUGGUGGGGGAAAUAGGUGCAU- -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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