miRNA: 3'- -GACGAGACGUGUUGGUCGGUGUGCCG- -5'
miRNA: 3'- -GACGAGACGuGu---UGGU---------------CGGUgUG-CCG- -5'
miRNA: 3'- gACGaGACGuGUUGGUC----GGUGUgCCG- -5'
miRNA: 3'- gACGAGA-CGUGuUGGUCGGUGu-----GCCG- -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 | |||||||
| 3382 | 3' | -55.9 | NC_001563.2 | + | 10880 | 1.12 | 4e-05 |
|
Target: 5'- uCUGCUCUGCACAACCAGCCACACGGCa -3' miRNA: 3'- -GACGAGACGUGUUGGUCGGUGUGCCG- -5' |
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| 3382 | 3' | -55.9 | NC_001563.2 | + | 7242 | 0.69 | 0.135536 |
|
Target: 5'- gCUGCUCUGCuCuuuuGCCAcuaugcuuacaugguGCCAgGCuGGCa -3' miRNA: 3'- -GACGAGACGuGu---UGGU---------------CGGUgUG-CCG- -5' |
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| 3382 | 3' | -55.9 | NC_001563.2 | + | 10023 | 0.67 | 0.188418 |
|
Target: 5'- gUGC-CUGC-CAACUGGguucCCACAgGGCg -3' miRNA: 3'- gACGaGACGuGUUGGUC----GGUGUgCCG- -5' |
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| 3382 | 3' | -55.9 | NC_001563.2 | + | 10955 | 0.78 | 0.023464 |
|
Target: 5'- gUGUUCUaGCACcACCAGCCACcuauguCGGCg -3' miRNA: 3'- gACGAGA-CGUGuUGGUCGGUGu-----GCCG- -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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