miRNA: 3'- cCGAGCaGCCUUGUCGaagUGGCAAG- -5'
miRNA: 3'- -CCGAGCAGCCUUGUCGAAGUGGCAAG- -5'
miRNA: 3'- -CCGaGCaGCCUUGUCG-----AAGUGGCa-AG- -5'
miRNA: 3'- -CCGagCAGCCUUGU--CGa-AGUGGCaag -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 | |||||||
| 1321 | 5' | -52.6 | NC_001331.1 | + | 6939 | 0.71 | 0.118684 |
|
Target: 5'- cGUUCGcCGGAACGGUgaaGCUGUUCc -3' miRNA: 3'- cCGAGCaGCCUUGUCGaagUGGCAAG- -5' |
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| 1321 | 5' | -52.6 | NC_001331.1 | + | 6898 | 1.12 | 6.7e-05 |
|
Target: 5'- cGGCUCGUCGGAACAGCUUCACCGUUCc -3' miRNA: 3'- -CCGAGCAGCCUUGUCGAAGUGGCAAG- -5' |
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| 1321 | 5' | -52.6 | NC_001331.1 | + | 2223 | 0.68 | 0.193313 |
|
Target: 5'- gGGC-CGgUGGAGCAGUucucuUUCGCCGggUCg -3' miRNA: 3'- -CCGaGCaGCCUUGUCG-----AAGUGGCa-AG- -5' |
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| 1321 | 5' | -52.6 | NC_001331.1 | + | 1727 | 0.67 | 0.240585 |
|
Target: 5'- aGGCg-GUCGGGGCGccGCcgUCACCGa-- -3' miRNA: 3'- -CCGagCAGCCUUGU--CGa-AGUGGCaag -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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