miRNA: 3'- uuAGC-GgUUCGuCUAGCUcUGCUGGC- -5'
miRNA: 3'- -UUAGCGGUU------CGUCuAGCucUgCUGGC- -5'
miRNA: 3'- uuaGCGGUUCGUCu-AGCU---------CUGCUGGc -5'
miRNA: 3'- uuaGCGGU----------UCGUCua-GCUC-UGCUGGC- -5'
miRNA: 3'- uuaGCGguUCGUCUAGCUcUGC--UGGC- -5'
Results 41 - 45 of 45 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 | |||||||
| 28140 | 5' | -53.6 | NC_005887.1 | + | 31341 | 0.66 | 0.732742 |
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Target: 5'- -cUCGaCgAGGC-GAUCGAcGCGGCCGa -3' miRNA: 3'- uuAGC-GgUUCGuCUAGCUcUGCUGGC- -5' |
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| 28140 | 5' | -53.6 | NC_005887.1 | + | 9304 | 0.66 | 0.743617 |
|
Target: 5'- cGAUCGCCGAcgcggcGCAGuUCGcuAgGACCGa -3' miRNA: 3'- -UUAGCGGUU------CGUCuAGCucUgCUGGC- -5' |
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| 28140 | 5' | -53.6 | NC_005887.1 | + | 18224 | 0.66 | 0.743617 |
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Target: 5'- --aUGCCGAGCAGcuUCGGcacgacgucGGCGGCCc -3' miRNA: 3'- uuaGCGGUUCGUCu-AGCU---------CUGCUGGc -5' |
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| 28140 | 5' | -53.6 | NC_005887.1 | + | 7493 | 0.66 | 0.743617 |
|
Target: 5'- --aCGCCAgcccaaacgaGGCGGcggCGGGuGCGACCGu -3' miRNA: 3'- uuaGCGGU----------UCGUCua-GCUC-UGCUGGC- -5' |
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| 28140 | 5' | -53.6 | NC_005887.1 | + | 17060 | 0.66 | 0.743617 |
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Target: 5'- --gCGCguGGCGGAUCGGcACGuaGCCGu -3' miRNA: 3'- uuaGCGguUCGUCUAGCUcUGC--UGGC- -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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