miRNA: 3'- -UGCCGCCG------UCCUUauaGUCGGCGUUg -5'
miRNA: 3'- -UGCCgCCGuCCUu-AUAGUCGG-CgUUG- -5'
miRNA: 3'- -UGCCGCCGUCCUUAua----GUcGGCGUUG- -5'
miRNA: 3'- -UGCCGCCG------------UCCuUAUAGUCGGCGUug -5'
miRNA: 3'- -UGCCGCCGUCCUUAUAGUCGGCGUUG- -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 | |||||||
| 8420 | 3' | -55.3 | NC_002166.1 | + | 20806 | 0.66 | 0.617958 |
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Target: 5'- aAUGGCGGCgcgguaAGGGA---CAGCCGUGGa -3' miRNA: 3'- -UGCCGCCG------UCCUUauaGUCGGCGUUg -5' |
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| 8420 | 3' | -55.3 | NC_002166.1 | + | 1434 | 0.68 | 0.453728 |
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Target: 5'- cGCGG-GGCuGGAucUGUCAGCCaGgAACg -3' miRNA: 3'- -UGCCgCCGuCCUu-AUAGUCGG-CgUUG- -5' |
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| 8420 | 3' | -55.3 | NC_002166.1 | + | 35878 | 0.71 | 0.324224 |
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Target: 5'- cGCGGCGGCGGGAGUcuggaaCGuCUGCGAUu -3' miRNA: 3'- -UGCCGCCGUCCUUAua----GUcGGCGUUG- -5' |
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| 8420 | 3' | -55.3 | NC_002166.1 | + | 3068 | 0.72 | 0.277782 |
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Target: 5'- aGCGGUGGCuuauuccugcuaAGG-AUGUUGGCCGCAu- -3' miRNA: 3'- -UGCCGCCG------------UCCuUAUAGUCGGCGUug -5' |
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| 8420 | 3' | -55.3 | NC_002166.1 | + | 5430 | 1.08 | 0.000643 |
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Target: 5'- aACGGCGGCAGGAAUAUCAGCCGCAACc -3' miRNA: 3'- -UGCCGCCGUCCUUAUAGUCGGCGUUG- -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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