miRNA: 3'- cuugAUGAGGUCGGcAUGgACCGGGc -5'
miRNA: 3'- cuUGAUGA---GGUCg-GCA---UGGACCG-GGC- -5'
miRNA: 3'- -CUUGA---UGAGGUCGGcauGGA-CCGGGc -5'
miRNA: 3'- cuUGAUG---AGG------------UCGGcAUGGACCGGGc -5'
miRNA: 3'- -CUUGAUGAGGUCGGCAUGGACCGGGC- -5'
Results 1 - 5 of 5 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 | |||||||
| 13034 | 5' | -57 | NC_003390.1 | + | 41629 | 0.66 | 0.586308 |
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Target: 5'- ---aUACUCUGGCCcUGCgUGGCCUu -3' miRNA: 3'- cuugAUGAGGUCGGcAUGgACCGGGc -5' |
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| 13034 | 5' | -57 | NC_003390.1 | + | 47511 | 0.66 | 0.564479 |
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Target: 5'- -uGCUACUggcCCAGagCGUgacGCCUGGCuCCGu -3' miRNA: 3'- cuUGAUGA---GGUCg-GCA---UGGACCG-GGC- -5' |
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| 13034 | 5' | -57 | NC_003390.1 | + | 30682 | 0.67 | 0.490185 |
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Target: 5'- aGGGCUcucGCUUCAGCCau-CCUcGGCCCc -3' miRNA: 3'- -CUUGA---UGAGGUCGGcauGGA-CCGGGc -5' |
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| 13034 | 5' | -57 | NC_003390.1 | + | 33912 | 0.67 | 0.479928 |
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Target: 5'- -uGCUGCgcgUCCcgcccgcgacguGGCC-UGCCUGGCCCu -3' miRNA: 3'- cuUGAUG---AGG------------UCGGcAUGGACCGGGc -5' |
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| 13034 | 5' | -57 | NC_003390.1 | + | 28143 | 1.08 | 0.000657 |
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Target: 5'- uGAACUACUCCAGCCGUACCUGGCCCGu -3' miRNA: 3'- -CUUGAUGAGGUCGGCAUGGACCGGGC- -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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