miRNA: 3'- aaGCCAuuuaAGUAGGuGGGCCGGUG- -5'
miRNA: 3'- aAGCCAuuuAAGU--AGGUGGGCC-GGUG- -5'
miRNA: 3'- aaGCC----AUUUaaGUAGGUGGgCCGGUG- -5'
miRNA: 3'- aaGCCAUUUAa-GUAGGUGGGCC-----GGUG- -5'
miRNA: 3'- -AAGCCAUUUAAGUAGGUGGGCCGGUG- -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 | |||||||
| 6146 | 5' | -52.5 | NC_001826.1 | + | 25081 | 0.67 | 0.926908 |
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Target: 5'- -gUGGUca--UCGUCCuCCUGGCCAUg -3' miRNA: 3'- aaGCCAuuuaAGUAGGuGGGCCGGUG- -5' |
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| 6146 | 5' | -52.5 | NC_001826.1 | + | 65154 | 0.67 | 0.921165 |
|
Target: 5'- cUUGGUu--UUCAcuUUCACCUGGgCCACa -3' miRNA: 3'- aAGCCAuuuAAGU--AGGUGGGCC-GGUG- -5' |
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| 6146 | 5' | -52.5 | NC_001826.1 | + | 4536 | 0.68 | 0.888506 |
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Target: 5'- -cUGGauuuUGAGagCAUCCACCaGGCCACg -3' miRNA: 3'- aaGCC----AUUUaaGUAGGUGGgCCGGUG- -5' |
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| 6146 | 5' | -52.5 | NC_001826.1 | + | 10592 | 0.69 | 0.832455 |
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Target: 5'- -cUGGUGGAUggUGUCCACCCGGgucccUCACa -3' miRNA: 3'- aaGCCAUUUAa-GUAGGUGGGCC-----GGUG- -5' |
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| 6146 | 5' | -52.5 | NC_001826.1 | + | 102115 | 1.08 | 0.005042 |
|
Target: 5'- aUUCGGUAAAUUCAUCCACCCGGCCACu -3' miRNA: 3'- -AAGCCAUUUAAGUAGGUGGGCCGGUG- -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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