miRNA: 3'- aAGCUUUCGAC-------GCGGCCCuaUgaCAG- -5'
miRNA: 3'- aAGCUUuC-GACGCGGCCCUAuGaCAG- -5'
miRNA: 3'- -AAGCUUUCGACGCGGCCCUAUGACAG- -5'
miRNA: 3'- aAGCUUu----CGACGCG---GCCCUAUG---ACAG- -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 |
| Predicted miRNA align pattern | |||||||
| 12121 | 5' | -54.2 | NC_003309.1 | + | 51424 | 0.68 | 0.606767 |
|
Target: 5'- gUCGAGAGCUGgaaacauCGCCGGGccAaaGUCc -3' miRNA: 3'- aAGCUUUCGAC-------GCGGCCCuaUgaCAG- -5' |
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| 12121 | 5' | -54.2 | NC_003309.1 | + | 44372 | 0.67 | 0.641826 |
|
Target: 5'- gUCGAAcGaCUGCGUCGGGAU-C-GUCc -3' miRNA: 3'- aAGCUUuC-GACGCGGCCCUAuGaCAG- -5' |
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| 12121 | 5' | -54.2 | NC_003309.1 | + | 13058 | 1.08 | 0.001145 |
|
Target: 5'- gUUCGAAAGCUGCGCCGGGAUACUGUCg -3' miRNA: 3'- -AAGCUUUCGACGCGGCCCUAUGACAG- -5' |
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| 12121 | 5' | -54.2 | NC_003309.1 | + | 5429 | 0.67 | 0.653132 |
|
Target: 5'- gUCGAAcuguuGUUGCGUcguCGGGAUAUcggUGUCa -3' miRNA: 3'- aAGCUUu----CGACGCG---GCCCUAUG---ACAG- -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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