miRNA: 3'- -UCGAGGuauUGACCU-----CGAa------GGAGGAC- -5'
miRNA: 3'- -UCGAGGuauuGAC-CUCGa---AGGAGGAC- -5'
miRNA: 3'- uCGAGGuauUGACCU-CGAAGGAGGac -5'
miRNA: 3'- -UCGAGGUAUUGACCUCGAAGGAGGAC- -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
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| Predicted miRNA align pattern | |||||||
| 10643 | 3' | -53.3 | NC_002702.1 | + | 32135 | 0.67 | 0.564325 |
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Target: 5'- uAGUUCCu--ACUGGAcuacgGCUgcaaauaCCUCCUGg -3' miRNA: 3'- -UCGAGGuauUGACCU-----CGAa------GGAGGAC- -5' |
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| 10643 | 3' | -53.3 | NC_002702.1 | + | 6193 | 0.71 | 0.363942 |
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Target: 5'- cAGCUCCuug-UUGaGAGCguacUCCUCCUGg -3' miRNA: 3'- -UCGAGGuauuGAC-CUCGa---AGGAGGAC- -5' |
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| 10643 | 3' | -53.3 | NC_002702.1 | + | 1057 | 0.72 | 0.319952 |
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Target: 5'- uGCUCC---GCUGGGcGUUUCCUCCg- -3' miRNA: 3'- uCGAGGuauUGACCU-CGAAGGAGGac -5' |
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| 10643 | 3' | -53.3 | NC_002702.1 | + | 21261 | 1.08 | 0.000803 |
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Target: 5'- aAGCUCCAUAACUGGAGCUUCCUCCUGc -3' miRNA: 3'- -UCGAGGUAUUGACCUCGAAGGAGGAC- -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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