miRNA: 3'- -UUUGCAUCUGUCCCAUGGGCAUCUCU- -5'
miRNA: 3'- -UUugCaUCUGUCCCa----UGGGC-AUCUCu -5'
miRNA: 3'- -UUUGCa-UCUGU-CCCAUGGGcAUCUCU- -5'
miRNA: 3'- -UUUGCau----CUGuCCCauGGGCAUCUCU- -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 | |||||||
| 12311 | 5' | -51.7 | NC_003323.1 | + | 7304 | 1.07 | 0.000227 |
|
Target: 5'- aAAACGUAGACAGGGUACCCGUAGAGAa -3' miRNA: 3'- -UUUGCAUCUGUCCCAUGGGCAUCUCU- -5' |
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| 12311 | 5' | -51.7 | NC_003323.1 | + | 4833 | 0.67 | 0.292999 |
|
Target: 5'- aGAugGaAGGCAGGGgcuggGCCUGaUGGAGc -3' miRNA: 3'- -UUugCaUCUGUCCCa----UGGGC-AUCUCu -5' |
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| 12311 | 5' | -51.7 | NC_003323.1 | + | 3234 | 0.72 | 0.128936 |
|
Target: 5'- gGAGCGaaGGACAgGGGUGCCUuUGGAGAc -3' miRNA: 3'- -UUUGCa-UCUGU-CCCAUGGGcAUCUCU- -5' |
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| 12311 | 5' | -51.7 | NC_003323.1 | + | 1171 | 0.69 | 0.209298 |
|
Target: 5'- gGGGCGgugaguGGCuGGGgcCCCGUGGGGGu -3' miRNA: 3'- -UUUGCau----CUGuCCCauGGGCAUCUCU- -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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