miRNA: 3'- -GACUCCCUCUACUCCCUCGACCGCCU- -5'
miRNA: 3'- -GACUCCC-UCU-----ACUCCCU------------CgaCCGCCU- -5'
miRNA: 3'- -GACUCCcUCUACUCCCuc----GACCG-CCU- -5'
miRNA: 3'- -GACUC---CCUCua--CUCCCUCGACCgCCu -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 | |||||||
| 28347 | 3' | -59.1 | NC_005946.1 | + | 12075 | 1.08 | 0.001014 |
|
Target: 5'- uCUGAGGGAGAUGAGGGAGCUGGCGGAg -3' miRNA: 3'- -GACUCCCUCUACUCCCUCGACCGCCU- -5' |
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| 28347 | 3' | -59.1 | NC_005946.1 | + | 12632 | 0.69 | 0.474101 |
|
Target: 5'- uCUGAGGGcAGAcgaccUGAGGGAcagccugccccaGgaGGUGGAg -3' miRNA: 3'- -GACUCCC-UCU-----ACUCCCU------------CgaCCGCCU- -5' |
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| 28347 | 3' | -59.1 | NC_005946.1 | + | 48475 | 0.7 | 0.446106 |
|
Target: 5'- cCUGAGGaAGAUGAGGGcucccuCUGGCaGGGg -3' miRNA: 3'- -GACUCCcUCUACUCCCuc----GACCG-CCU- -5' |
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| 28347 | 3' | -59.1 | NC_005946.1 | + | 85262 | 0.73 | 0.299935 |
|
Target: 5'- uCUGAGcuuGGGGcuugGAGGGAGCUGGgGGc -3' miRNA: 3'- -GACUC---CCUCua--CUCCCUCGACCgCCu -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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