miRNA: 3'- aGCCUGCCGGaCUuaUGGCUAC-GCGa -5'
miRNA: 3'- -AGCCUGCCgGACUUAuGGCUa------CGCGa -5'
miRNA: 3'- -AGCcUGC-CGGACuua--UGGCUACG-CGa -5'
miRNA: 3'- agCCUGCCGGa--C-UUAUGGCuaCGCGA- -5'
miRNA: 3'- aGCC---UGCCGGa-----CUUA---UGGCuaCGCGa -5'
Results 21 - 25 of 25 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 | |||||||
| 28013 | 3' | -55.6 | NC_005887.1 | + | 35076 | 0.77 | 0.130799 |
|
Target: 5'- gCGGGCGGCCgGG--GCCGAUGuCGCg -3' miRNA: 3'- aGCCUGCCGGaCUuaUGGCUAC-GCGa -5' |
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| 28013 | 3' | -55.6 | NC_005887.1 | + | 35101 | 0.66 | 0.625629 |
|
Target: 5'- uUCGGGCGG-UUGAAUuUCGAgggcgggGCGCg -3' miRNA: 3'- -AGCCUGCCgGACUUAuGGCUa------CGCGa -5' |
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| 28013 | 3' | -55.6 | NC_005887.1 | + | 36827 | 0.67 | 0.581018 |
|
Target: 5'- aUCGuGCGuGCCUGcugcgGCCGGUGCuGCg -3' miRNA: 3'- -AGCcUGC-CGGACuua--UGGCUACG-CGa -5' |
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| 28013 | 3' | -55.6 | NC_005887.1 | + | 39404 | 0.71 | 0.342392 |
|
Target: 5'- -aGGAUGGUCgcgGcGGUGCCGcgGCGCUu -3' miRNA: 3'- agCCUGCCGGa--C-UUAUGGCuaCGCGA- -5' |
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| 28013 | 3' | -55.6 | NC_005887.1 | + | 41999 | 0.67 | 0.537101 |
|
Target: 5'- aCGGccuGCGGCCcacgucGAGUgucGCCGcgGCGCg -3' miRNA: 3'- aGCC---UGCCGGa-----CUUA---UGGCuaCGCGa -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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