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Acc. No. | Name | Perfect MFE.* | RefSeq Acc. | strand | Start Position | R_P_ratio# | P value |
Predicted miRNA align pattern | |||||||
MIMAT0002192 | kshv-miR-K12-4-3p | -45.5 | NC_003409.1 | - | 101412 | 0.66 | 0.999593 |
Target: 5'- gCAGUUGGGCaaCAGUAUUUa- -3' miRNA: 3'- aGUCGAUCCGgaGUCAUAAGau -5' |
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MIMAT0002192 | kshv-miR-K12-4-3p | -45.5 | NC_003409.1 | - | 60768 | 0.67 | 0.998044 |
Target: 5'- -aGGCUAguGGUCUgGGUGUUCUGa -3' miRNA: 3'- agUCGAU--CCGGAgUCAUAAGAU- -5' |
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MIMAT0002192 | kshv-miR-K12-4-3p | -45.5 | NC_003409.1 | + | 121295 | 1.01 | 0.040964 |
Target: 5'- aUCAGCUAGGCCUCAGUAUUCUAu -3' miRNA: 3'- -AGUCGAUCCGGAGUCAUAAGAU- -5' |
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MIMAT0002192 | kshv-miR-K12-4-3p | -45.5 | NC_003409.1 | + | 113579 | 0.71 | 0.966299 |
Target: 5'- gUCAGCUGGGCCUCAu------- -3' miRNA: 3'- -AGUCGAUCCGGAGUcauaagau -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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