miRNA: 3'- -UGCCGCUCCUCACGCAGCUCUAUGGG- -5'
miRNA: 3'- -UGCCGCUCCuCA-CGCAGCuCU-----------AUGGG- -5'
miRNA: 3'- uGCCGCUCCUCA-CGCAGC----UCUAuGGG- -5'
miRNA: 3'- -UGCCGcu-CCUcaCGCAGCuCuAUGGG- -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 | |||||||
| 9797 | 3' | -56.2 | NC_002593.1 | + | 67678 | 1.12 | 0.001195 |
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Target: 5'- gACGGCGAGGAGUGCGUCGAGAUACCCg -3' miRNA: 3'- -UGCCGCUCCUCACGCAGCUCUAUGGG- -5' |
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| 9797 | 3' | -56.2 | NC_002593.1 | + | 29562 | 0.73 | 0.469496 |
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Target: 5'- gACGGCGAGG-GUcGCGUCGuGGcgcacgccuacUAUCCg -3' miRNA: 3'- -UGCCGCUCCuCA-CGCAGCuCU-----------AUGGG- -5' |
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| 9797 | 3' | -56.2 | NC_002593.1 | + | 67514 | 0.71 | 0.53818 |
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Target: 5'- uCGGUGAGGGGUaGCGUCGuguuGGGU-UCCg -3' miRNA: 3'- uGCCGCUCCUCA-CGCAGC----UCUAuGGG- -5' |
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| 9797 | 3' | -56.2 | NC_002593.1 | + | 69703 | 0.68 | 0.743215 |
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Target: 5'- gGCGGCuuuGGAcaGCGUCGuG-UACCCg -3' miRNA: 3'- -UGCCGcu-CCUcaCGCAGCuCuAUGGG- -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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