miRNA: 3'- gaaCUGCCCUcCCAGCAuCUuuGUUG- -5'
miRNA: 3'- -GAACUGCC-CUCCC--AGCaucuUUGUUG- -5'
miRNA: 3'- gaacUGCC----CUCCCAGCAUCU-UUGUUG- -5'
miRNA: 3'- gaaCUGC-CCUCCCAGCAucuuUGUUG- -5'
miRNA: 3'- -GAACUGCCCUCCCAGCAUCUUUGUUG- -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 | |||||||
| 1359 | 3' | -50 | NC_001335.1 | + | 3060 | 0.66 | 0.932616 |
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Target: 5'- --aGGCGGGAaGGUCGUuGAcgUGACc -3' miRNA: 3'- gaaCUGCCCUcCCAGCAuCUuuGUUG- -5' |
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| 1359 | 3' | -50 | NC_001335.1 | + | 18741 | 0.67 | 0.9143 |
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Target: 5'- uCUUGACGGuGGGGGacUCG----AACAGCg -3' miRNA: 3'- -GAACUGCC-CUCCC--AGCaucuUUGUUG- -5' |
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| 1359 | 3' | -50 | NC_001335.1 | + | 34960 | 0.69 | 0.815698 |
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Target: 5'- ---aACGGucgaGAGGGUCGUGGAcGGCAAUc -3' miRNA: 3'- gaacUGCC----CUCCCAGCAUCU-UUGUUG- -5' |
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| 1359 | 3' | -50 | NC_001335.1 | + | 18404 | 0.71 | 0.743368 |
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Target: 5'- --aGACGuGGAGGGUUGUuucuACGACc -3' miRNA: 3'- gaaCUGC-CCUCCCAGCAucuuUGUUG- -5' |
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| 1359 | 3' | -50 | NC_001335.1 | + | 18492 | 1.1 | 0.003046 |
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Target: 5'- cCUUGACGGGAGGGUCGUAGAAACAACc -3' miRNA: 3'- -GAACUGCCCUCCCAGCAUCUUUGUUG- -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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