miRNA: 3'- -CGACUAACGACUCGCGCGGCGAGGAC- -5'
miRNA: 3'- -CGACUA--ACGacUCGCGCGgCGa---GGac -5'
miRNA: 3'- -CGaCUa--ACGACUCG----CGCGG---CGAGGAC- -5'
miRNA: 3'- -CGACUa-----ACGAC---UCGCG-CGG------------CGAGGac -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 |
| Predicted miRNA align pattern | |||||||
| 30497 | 3' | -57.3 | NC_006548.1 | + | 3776 | 1.09 | 0.000338 |
|
Target: 5'- uGCUGAUUGCUGAGCGCGCCGCUCCUGc -3' miRNA: 3'- -CGACUAACGACUCGCGCGGCGAGGAC- -5' |
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| 30497 | 3' | -57.3 | NC_006548.1 | + | 11756 | 0.66 | 0.44784 |
|
Target: 5'- aGCUGGUcaUGCgcGGCGCGCgGCggcgCCg- -3' miRNA: 3'- -CGACUA--ACGacUCGCGCGgCGa---GGac -5' |
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| 30497 | 3' | -57.3 | NC_006548.1 | + | 12065 | 0.68 | 0.354201 |
|
Target: 5'- cGCcGAgcaUGCUGGGUcgguGCGCUgauGCUCCUGc -3' miRNA: 3'- -CGaCUa--ACGACUCG----CGCGG---CGAGGAC- -5' |
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| 30497 | 3' | -57.3 | NC_006548.1 | + | 12939 | 0.67 | 0.428013 |
|
Target: 5'- cGCUGAgcgcggUGCUGugcGGCGCaGCCguggugaccacgGCUCCg- -3' miRNA: 3'- -CGACUa-----ACGAC---UCGCG-CGG------------CGAGGac -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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