miRNA: 3'- -GCCa-UGGCGGCCUUaGCCaUGCauuu -5'
miRNA: 3'- -GCC---AUGGCGGCCUuagCCAUGCAUuu -5'
miRNA: 3'- -GCCAUGG-CGGCCUUag---CCAUGcauuu -5'
miRNA: 3'- gCCAUGGCGGCCUUAGCcaUGcauuu -5'
miRNA: 3'- -GCCAUGGCGGCCUUAGCCAUGCAUUU- -5'
Results 1 - 5 of 5 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 | |||||||
| 13570 | 3' | -52.6 | NC_003444.1 | + | 8106 | 0.68 | 0.615959 |
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Target: 5'- aCGGggACCGCCGGAA-CGG-GCGc--- -3' miRNA: 3'- -GCCa-UGGCGGCCUUaGCCaUGCauuu -5' |
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| 13570 | 3' | -52.6 | NC_003444.1 | + | 11443 | 0.69 | 0.54763 |
|
Target: 5'- cCGGaucUACCGCCGGAuaaGGUGUGUAu- -3' miRNA: 3'- -GCC---AUGGCGGCCUuagCCAUGCAUuu -5' |
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| 13570 | 3' | -52.6 | NC_003444.1 | + | 24737 | 0.71 | 0.440214 |
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Target: 5'- aCGGUACCaGCCGGAAgcaagGGUACa---- -3' miRNA: 3'- -GCCAUGG-CGGCCUUag---CCAUGcauuu -5' |
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| 13570 | 3' | -52.6 | NC_003444.1 | + | 14546 | 0.74 | 0.312342 |
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Target: 5'- uGGUGCCGCCGGAGUCGc-ACa---- -3' miRNA: 3'- gCCAUGGCGGCCUUAGCcaUGcauuu -5' |
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| 13570 | 3' | -52.6 | NC_003444.1 | + | 36460 | 1.07 | 0.001725 |
|
Target: 5'- aCGGUACCGCCGGAAUCGGUACGUAAAc -3' miRNA: 3'- -GCCAUGGCGGCCUUAGCCAUGCAUUU- -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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