miRNA: 3'- -UACCGGGGgaGCG-UGCAC-CUAUUCCA- -5'
miRNA: 3'- uACCGgGGGa----GCGUGCaCCu---AUUCCA- -5'
miRNA: 3'- uaCCGgGGGAGCGuGCA-----------CCUAUUCCA- -5'
miRNA: 3'- uACcGGGGGAGCGugCACCUauucca -5'
miRNA: 3'- -UACCGGGGGAGCGUGCACCUAUUCCA- -5'
Results 1 - 5 of 5 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 | |||||||
| 1720 | 5' | -58.5 | NC_001347.2 | + | 160818 | 0.66 | 0.857774 |
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Target: 5'- uGUGGCUCUgaUGCuGCGUGaGGUAGGGUc -3' miRNA: 3'- -UACCGGGGgaGCG-UGCAC-CUAUUCCA- -5' |
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| 1720 | 5' | -58.5 | NC_001347.2 | + | 138196 | 0.67 | 0.834493 |
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Target: 5'- uUGGCgCCCguaggCGCGCG-GGuuuuUGGGGUg -3' miRNA: 3'- uACCGgGGGa----GCGUGCaCCu---AUUCCA- -5' |
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| 1720 | 5' | -58.5 | NC_001347.2 | + | 100758 | 0.68 | 0.783459 |
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Target: 5'- -gGGCgUCCUCGCcCGUcgauagcucuuGGGUGAGGUu -3' miRNA: 3'- uaCCGgGGGAGCGuGCA-----------CCUAUUCCA- -5' |
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| 1720 | 5' | -58.5 | NC_001347.2 | + | 78303 | 0.7 | 0.65954 |
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Target: 5'- cUGaCCCCCUCGCugGUGGAc----- -3' miRNA: 3'- uACcGGGGGAGCGugCACCUauucca -5' |
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| 1720 | 5' | -58.5 | NC_001347.2 | + | 82929 | 1.05 | 0.003936 |
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Target: 5'- cAUGGCCCCCUCGCACGUGGAUAAGGUg -3' miRNA: 3'- -UACCGGGGGAGCGUGCACCUAUUCCA- -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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