miRNA: 3'- -CGUGCGGCUUAGaa-GAGg-----C-AGUGauu -5'
miRNA: 3'- -CGUgCGGCUuaGaa-Ga----GGCAGUGAUu -5'
miRNA: 3'- -CGUGCgGCuu-AGAAGAGGCAG---UGAuu -5'
miRNA: 3'- cGUGcGGCUUA----GAAGAGGCAGUGauu -5'
miRNA: 3'- -CGUGCGGCUUAGAAGAGGCAGUGAUU- -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 | |||||||
| 18199 | 3' | -50.9 | NC_004680.1 | + | 40518 | 0.66 | 0.926141 |
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Target: 5'- cGCACGCCGGAUCggaCUCgauguaGaUCACa-- -3' miRNA: 3'- -CGUGCGGCUUAGaa-GAGg-----C-AGUGauu -5' |
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| 18199 | 3' | -50.9 | NC_004680.1 | + | 31577 | 0.67 | 0.869386 |
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Target: 5'- aGCAgGCCGAcgUgcgCaggagCCGUCACUAc -3' miRNA: 3'- -CGUgCGGCUuaGaa-Ga----GGCAGUGAUu -5' |
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| 18199 | 3' | -50.9 | NC_004680.1 | + | 35176 | 0.67 | 0.86105 |
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Target: 5'- cGCGCGgUGuucUCUUCUCCGUCugaGCUu- -3' miRNA: 3'- -CGUGCgGCuu-AGAAGAGGCAG---UGAuu -5' |
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| 18199 | 3' | -50.9 | NC_004680.1 | + | 8059 | 0.71 | 0.70015 |
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Target: 5'- cCGCaCCGAGUacgaCUUCUCCGUCACc-- -3' miRNA: 3'- cGUGcGGCUUA----GAAGAGGCAGUGauu -5' |
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| 18199 | 3' | -50.9 | NC_004680.1 | + | 32255 | 1.09 | 0.003112 |
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Target: 5'- aGCACGCCGAAUCUUCUCCGUCACUAAc -3' miRNA: 3'- -CGUGCGGCUUAGAAGAGGCAGUGAUU- -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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