miRNA: 3'- agUGCGGUa----CCUGGUGa------GUCGUGUac -5'
miRNA: 3'- -AGUGCGGUACCUGGUGAGUCGUGUAC- -5'
miRNA: 3'- aGUGCGG-------UACCUGguga--GUCGUGUAC- -5'
miRNA: 3'- aGUGCGGUaccUGGUGA-----GUCGUGUAc -5'
miRNA: 3'- -AGUgCGGUACC---------UGGUGA---GUCGUGUAc -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 | |||||||
| 21745 | 5' | -54.2 | NC_004813.1 | + | 35690 | 0.69 | 0.577669 |
|
Target: 5'- -aGCGCCGggaaaGGACCACcacauugCGGCGCAg- -3' miRNA: 3'- agUGCGGUa----CCUGGUGa------GUCGUGUac -5' |
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| 21745 | 5' | -54.2 | NC_004813.1 | + | 35408 | 1.09 | 0.001126 |
|
Target: 5'- gUCACGCCAUGGACCACUCAGCACAUGa -3' miRNA: 3'- -AGUGCGGUACCUGGUGAGUCGUGUAC- -5' |
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| 21745 | 5' | -54.2 | NC_004813.1 | + | 33056 | 0.67 | 0.720431 |
|
Target: 5'- cCACGCUgcugagaAUGGACagugagCGGCGCAUGa -3' miRNA: 3'- aGUGCGG-------UACCUGguga--GUCGUGUAC- -5' |
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| 21745 | 5' | -54.2 | NC_004813.1 | + | 31288 | 0.66 | 0.784202 |
|
Target: 5'- aCGCGCCAcc-ACCGCUuccgcCAGCGCAUu -3' miRNA: 3'- aGUGCGGUaccUGGUGA-----GUCGUGUAc -5' |
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| 21745 | 5' | -54.2 | NC_004813.1 | + | 15187 | 0.69 | 0.588727 |
|
Target: 5'- aUCAgGCCGUGGguggaaaaaGCCGCUgagCAGUGCAUa -3' miRNA: 3'- -AGUgCGGUACC---------UGGUGA---GUCGUGUAc -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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