miRNA: 3'- -CUUUCUuuGCGgUaCUUUGCA--CGCGG- -5'
miRNA: 3'- -CUUUCUUUG-CGGU-----ACUUUGCA----CGCGG- -5'
miRNA: 3'- -CUUUCUUUGCGGUACUUUGCACGCGG- -5'
Results 1 - 3 of 3 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 | |||||||
| 13903 | 3' | -47.4 | NC_003501.1 | + | 3001 | 0.67 | 0.576731 |
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Target: 5'- cGAAAGA--CGCgAcGAGAUGUucGCGCCu -3' miRNA: 3'- -CUUUCUuuGCGgUaCUUUGCA--CGCGG- -5' |
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| 13903 | 3' | -47.4 | NC_003501.1 | + | 5951 | 0.72 | 0.294257 |
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Target: 5'- aGAAGGAAGCgGCCAugucaUGGAACGUuacuGUGUCa -3' miRNA: 3'- -CUUUCUUUG-CGGU-----ACUUUGCA----CGCGG- -5' |
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| 13903 | 3' | -47.4 | NC_003501.1 | + | 9656 | 1.14 | 0.000293 |
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Target: 5'- cGAAAGAAACGCCAUGAAACGUGCGCCu -3' miRNA: 3'- -CUUUCUUUGCGGUACUUUGCACGCGG- -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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