miRNA: 3'- cuuaUCGU---------------AGGGUcg--CUCUUGGGUUC- -5'
miRNA: 3'- cuuaUCGU-AGGGUCGCU-CUUGGGuUC- -5'
miRNA: 3'- cuUAUCGUAg-------GGUCGCUCuUGGGUuc -5'
miRNA: 3'- cuuauCGUAGGGUCGCUCuUGGGuUC- -5'
miRNA: 3'- -CUUAUCGUAGGGUCGCUCUUGGGUUC- -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 | |||||||
| 12051 | 5' | -51.1 | NC_003298.1 | + | 22412 | 0.67 | 0.780114 |
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Target: 5'- ---aAGCAaaaaaccccucagacUCCCAaagaGGGAACCCAAGg -3' miRNA: 3'- cuuaUCGU---------------AGGGUcg--CUCUUGGGUUC- -5' |
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| 12051 | 5' | -51.1 | NC_003298.1 | + | 31461 | 0.67 | 0.754066 |
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Target: 5'- ---aGGCGuUCUUAGCGAaGAACCCuAGg -3' miRNA: 3'- cuuaUCGU-AGGGUCGCU-CUUGGGuUC- -5' |
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| 12051 | 5' | -51.1 | NC_003298.1 | + | 32266 | 0.71 | 0.511493 |
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Target: 5'- -cAUAGCAUagaaaccaCCAGCGAG-ACCCAu- -3' miRNA: 3'- cuUAUCGUAg-------GGUCGCUCuUGGGUuc -5' |
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| 12051 | 5' | -51.1 | NC_003298.1 | + | 2723 | 0.71 | 0.500348 |
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Target: 5'- ----cGCAUCCUAGCGAGuACCUuAGc -3' miRNA: 3'- cuuauCGUAGGGUCGCUCuUGGGuUC- -5' |
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| 12051 | 5' | -51.1 | NC_003298.1 | + | 35195 | 1.1 | 0.001153 |
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Target: 5'- cGAAUAGCAUCCCAGCGAGAACCCAAGg -3' miRNA: 3'- -CUUAUCGUAGGGUCGCUCUUGGGUUC- -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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