miRNA: 3'- -CG-AC-UCGCGAcagCCGGAA--------CCGCCGU- -5'
miRNA: 3'- -CGACUCGCGACaGCCGGa-----ACCG-CCGU- -5'
miRNA: 3'- cgaCUCGCG-ACAg---CCGGAACCGCCGu -5'
miRNA: 3'- -CG-ACUCGCGACAGCCGGAACCGCCGU- -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 | |||||||
| 21866 | 3' | -60.2 | NC_004902.1 | + | 23740 | 0.66 | 0.368252 |
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Target: 5'- uGCuUGaAGCGCUuagGGCCUUccgaugucGGCGGCAg -3' miRNA: 3'- -CG-AC-UCGCGAcagCCGGAA--------CCGCCGU- -5' |
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| 21866 | 3' | -60.2 | NC_004902.1 | + | 8358 | 0.73 | 0.134332 |
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Target: 5'- uGCUGGGUGUUGaUGGCCgucgucUGGCgGGCAc -3' miRNA: 3'- -CGACUCGCGACaGCCGGa-----ACCG-CCGU- -5' |
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| 21866 | 3' | -60.2 | NC_004902.1 | + | 34880 | 0.74 | 0.098827 |
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Target: 5'- --gGGGCGCuUGUgaaaGGCCUUGGCGGUc -3' miRNA: 3'- cgaCUCGCG-ACAg---CCGGAACCGCCGu -5' |
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| 21866 | 3' | -60.2 | NC_004902.1 | + | 24417 | 1.03 | 0.000593 |
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Target: 5'- cGCgUGAGCGCUGUCGGCCUUGGCGGCAc -3' miRNA: 3'- -CG-ACUCGCGACAGCCGGAACCGCCGU- -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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