miRNA: 3'- ggUCCC-GCUUG---CGCuGACGUCGAaua -5'
miRNA: 3'- -GGUCCCGCu--UGCGCUGac-----------GUCGAAUa -5'
miRNA: 3'- -GGUC---------CCGCUugCGCUGa-----CGUCGAAUa -5'
miRNA: 3'- gGuCCCGC-UUGCGCUGA--CGUCGaaua -5'
miRNA: 3'- -GGUCCCGCUUGCGCUGACGUCGAAUA- -5'
Results 21 - 25 of 25 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 | |||||||
| 10359 | 3' | -55 | NC_002687.1 | + | 159711 | 0.69 | 0.934936 |
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Target: 5'- -gAGGGcCGAGCacaGCGcCUGCAGCUg-- -3' miRNA: 3'- ggUCCC-GCUUG---CGCuGACGUCGAaua -5' |
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| 10359 | 3' | -55 | NC_002687.1 | + | 35586 | 0.69 | 0.927015 |
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Target: 5'- aUCGGGGCGuguACGCGGCgcaauugcuuccaCAGCUUGg -3' miRNA: 3'- -GGUCCCGCu--UGCGCUGac-----------GUCGAAUa -5' |
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| 10359 | 3' | -55 | NC_002687.1 | + | 318637 | 0.7 | 0.914064 |
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Target: 5'- aCCAGagaugcaaaGGCGGugGCGGCguaagcGUAGCUUGg -3' miRNA: 3'- -GGUC---------CCGCUugCGCUGa-----CGUCGAAUa -5' |
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| 10359 | 3' | -55 | NC_002687.1 | + | 12251 | 0.72 | 0.806131 |
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Target: 5'- aCuGGGCGuGACGCGGCUgcGCAGCg--- -3' miRNA: 3'- gGuCCCGC-UUGCGCUGA--CGUCGaaua -5' |
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| 10359 | 3' | -55 | NC_002687.1 | + | 200396 | 1.08 | 0.008467 |
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Target: 5'- gCCAGGGCGAACGCGACUGCAGCUUAUg -3' miRNA: 3'- -GGUCCCGCUUGCGCUGACGUCGAAUA- -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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