miRNA: 3'- agGcCCUCAGAuagg--UCAAACCGUUG- -5'
miRNA: 3'- -AGGCC----CUCAGAU--AGGUCAaa--C-CGUUG- -5'
miRNA: 3'- -AGGCCCUCa----GAUAGgUCAAACCg-UUG- -5'
miRNA: 3'- -AGGCCCUCAGAUAGGUCAAACCGUUG- -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
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| Predicted miRNA align pattern | |||||||
| 21015 | 5' | -51.9 | NC_004735.1 | + | 102409 | 0.66 | 0.971686 |
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Target: 5'- -aCuGGAGUCUuuacgaAGUUUGGCGGCg -3' miRNA: 3'- agGcCCUCAGAuagg--UCAAACCGUUG- -5' |
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| 21015 | 5' | -51.9 | NC_004735.1 | + | 28965 | 0.67 | 0.965367 |
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Target: 5'- aUCCGGagacGGGUCUGgcUCCGGUgggaGcGCGGCg -3' miRNA: 3'- -AGGCC----CUCAGAU--AGGUCAaa--C-CGUUG- -5' |
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| 21015 | 5' | -51.9 | NC_004735.1 | + | 17483 | 0.67 | 0.965367 |
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Target: 5'- uUUCGGGAGaauagUUAUCgAGUUUGGagAACa -3' miRNA: 3'- -AGGCCCUCa----GAUAGgUCAAACCg-UUG- -5' |
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| 21015 | 5' | -51.9 | NC_004735.1 | + | 73347 | 1.1 | 0.004822 |
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Target: 5'- aUCCGGGAGUCUAUCCAGUUUGGCAACc -3' miRNA: 3'- -AGGCCCUCAGAUAGGUCAAACCGUUG- -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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