miRNA: 3'- gCUCGC----CCAGUUGU--CGUUGGCGACGu -5'
miRNA: 3'- -GCU--CGCCCAGU---UGUCGUUG-GCGACGU- -5'
miRNA: 3'- -GCUCGCCCA-GUUGUCGU--UGGCGa---CGU- -5'
miRNA: 3'- -GCUCGCCCAGUUGUCGUUGGCGACGU- -5'
Results 21 - 24 of 24 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 | |||||||
| 27563 | 5' | -56.5 | NC_005882.1 | + | 35822 | 0.73 | 0.194593 |
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Target: 5'- gGAGUGuugcGGUCAGCGucGCGAUCGCUGCc -3' miRNA: 3'- gCUCGC----CCAGUUGU--CGUUGGCGACGu -5' |
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| 27563 | 5' | -56.5 | NC_005882.1 | + | 33102 | 0.74 | 0.16934 |
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Target: 5'- gCGAauGCGGGUCGggcGCGGCGAUaUGCUGCGc -3' miRNA: 3'- -GCU--CGCCCAGU---UGUCGUUG-GCGACGU- -5' |
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| 27563 | 5' | -56.5 | NC_005882.1 | + | 3542 | 0.81 | 0.054316 |
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Target: 5'- gCGAGCGGGUaCAGCAGCGacACCGUuucgGCAc -3' miRNA: 3'- -GCUCGCCCA-GUUGUCGU--UGGCGa---CGU- -5' |
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| 27563 | 5' | -56.5 | NC_005882.1 | + | 4757 | 1.09 | 0.000418 |
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Target: 5'- gCGAGCGGGUCAACAGCAACCGCUGCAg -3' miRNA: 3'- -GCUCGCCCAGUUGUCGUUGGCGACGU- -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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