miRNA: 3'- -UCGGugAGGA--A---------------GGCCAUuaUCGCGUu -5'
miRNA: 3'- -UCGG-UGAgGaa--GGCCAUuaUCGCGuu -5'
miRNA: 3'- uCGGUGAGG---AAGGCCauUAUCGCguu -5'
miRNA: 3'- uCGGUGAGGAAGGCCauuaUC-GCGuu -5'
miRNA: 3'- -UCGGUGAGGAAGGCCAUUAUCGCGUU- -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 | |||||||
| 30427 | 5' | -53.8 | NC_006548.1 | + | 14896 | 0.66 | 0.636234 |
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Target: 5'- cGGCCugUCCUggUccaccgccuaugcugCCGGUG--AGCGCAc -3' miRNA: 3'- -UCGGugAGGA--A---------------GGCCAUuaUCGCGUu -5' |
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| 30427 | 5' | -53.8 | NC_006548.1 | + | 1199 | 0.66 | 0.631573 |
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Target: 5'- gAGCCgGCUgCaaagCCGGUAcgGGCGCu- -3' miRNA: 3'- -UCGG-UGAgGaa--GGCCAUuaUCGCGuu -5' |
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| 30427 | 5' | -53.8 | NC_006548.1 | + | 14433 | 0.68 | 0.505763 |
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Target: 5'- cGCCGCUCCagcUUCUGGccGUAGCGa-- -3' miRNA: 3'- uCGGUGAGG---AAGGCCauUAUCGCguu -5' |
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| 30427 | 5' | -53.8 | NC_006548.1 | + | 34505 | 0.71 | 0.363841 |
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Target: 5'- uGCCAUUCCUUCCGGgca-AGuCGCc- -3' miRNA: 3'- uCGGUGAGGAAGGCCauuaUC-GCGuu -5' |
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| 30427 | 5' | -53.8 | NC_006548.1 | + | 10738 | 1.06 | 0.001033 |
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Target: 5'- cAGCCACUCCUUCCGGUAAUAGCGCAAa -3' miRNA: 3'- -UCGGUGAGGAAGGCCAUUAUCGCGUU- -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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