miRNA: 3'- gCUAGACC---UACUcaUGGAGaUGCGGg -5'
miRNA: 3'- -GCUAGACCu-ACUCAuGGAgA-----UGCGGg -5'
miRNA: 3'- -GCuAGACCu--ACU---------CAUGGAGAUGCGGG- -5'
miRNA: 3'- -GCUAGACCUACUCAUGGAGAUGCGGG- -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 | |||||||
| 21994 | 3' | -52 | NC_004914.1 | + | 12976 | 0.69 | 0.787452 |
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Target: 5'- gGAUCUGGucaAUGAugGCCUUcACGCCg -3' miRNA: 3'- gCUAGACC---UACUcaUGGAGaUGCGGg -5' |
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| 21994 | 3' | -52 | NC_004914.1 | + | 44684 | 0.69 | 0.767321 |
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Target: 5'- gCGAUCUGGuuUGAGU-CCUgUuucaaACGCCa -3' miRNA: 3'- -GCUAGACCu-ACUCAuGGAgA-----UGCGGg -5' |
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| 21994 | 3' | -52 | NC_004914.1 | + | 58719 | 0.7 | 0.736097 |
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Target: 5'- cCGuUCUGGcgcUGAuugccgcagGUGCUUCUGCGCCUg -3' miRNA: 3'- -GCuAGACCu--ACU---------CAUGGAGAUGCGGG- -5' |
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| 21994 | 3' | -52 | NC_004914.1 | + | 24920 | 1.14 | 0.001349 |
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Target: 5'- cCGAUCUGGAUGAGUACCUCUACGCCCg -3' miRNA: 3'- -GCUAGACCUACUCAUGGAGAUGCGGG- -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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