miRNA: 3'- cACUGGACCGu----CCCGaguuuGAGCuG- -5'
miRNA: 3'- cacUGGACCGUCC------CGAGuuUGAGCUG- -5'
miRNA: 3'- caCUGG-----ACCGUCCCG-----AGUUUG------AGCUG- -5'
miRNA: 3'- -CACUGGACCGUCCCGAGUUUGAGCUG- -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 | |||||||
| 31600 | 5' | -55.4 | NC_006875.1 | + | 1603 | 0.66 | 0.175526 |
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Target: 5'- cUGACCUGGCuccgcGGGCgu---CUCGuCg -3' miRNA: 3'- cACUGGACCGu----CCCGaguuuGAGCuG- -5' |
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| 31600 | 5' | -55.4 | NC_006875.1 | + | 4710 | 0.68 | 0.118742 |
|
Target: 5'- --cGCCUGGCGGGcaucguGCUCu-ACUUGACc -3' miRNA: 3'- cacUGGACCGUCC------CGAGuuUGAGCUG- -5' |
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| 31600 | 5' | -55.4 | NC_006875.1 | + | 350 | 0.69 | 0.100546 |
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Target: 5'- -gGGCCgucagUGGCAGGGUcuuccUCAAGCagccaaUCGACa -3' miRNA: 3'- caCUGG-----ACCGUCCCG-----AGUUUG------AGCUG- -5' |
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| 31600 | 5' | -55.4 | NC_006875.1 | + | 2163 | 1.08 | 4.7e-05 |
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Target: 5'- uGUGACCUGGCAGGGCUCAAACUCGACc -3' miRNA: 3'- -CACUGGACCGUCCCGAGUUUGAGCUG- -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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