miRNA: 3'- -CCUGCCGUCGACAGAGAGGGAGUUGA- -5'
miRNA: 3'- cCUGCCGUCGACaGAGAGGGaguuga -5'
miRNA: 3'- -CCUGcCGUCGacaGAGAGGGa-GUUGa -5'
miRNA: 3'- -CCugC-CGUCGACa-----GAGagGGAGUUGa -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 | |||||||
| 347 | 5' | -55.6 | AC_000011.1 | + | 4901 | 1.1 | 0.00041 |
|
Target: 5'- aGGACGGCAGCUGUCUCUCCCUCAACUa -3' miRNA: 3'- -CCUGCCGUCGACAGAGAGGGAGUUGA- -5' |
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| 347 | 5' | -55.6 | AC_000011.1 | + | 25738 | 0.66 | 0.563855 |
|
Target: 5'- uGGCGGCGGCUGcUUCUUCCa----- -3' miRNA: 3'- cCUGCCGUCGACaGAGAGGGaguuga -5' |
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| 347 | 5' | -55.6 | AC_000011.1 | + | 13258 | 0.66 | 0.552731 |
|
Target: 5'- uGGACaGCAGCgugUUCUCCCccCGACc -3' miRNA: 3'- -CCUGcCGUCGacaGAGAGGGa-GUUGa -5' |
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| 347 | 5' | -55.6 | AC_000011.1 | + | 27106 | 0.66 | 0.597541 |
|
Target: 5'- uGGugGcGCAGCUGaccuagCUCggCUUCGACa -3' miRNA: 3'- -CCugC-CGUCGACa-----GAGagGGAGUUGa -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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