miRNA: 3'- agaCGcgUACCGCGG---GCGCCUUUUUU- -5'
miRNA: 3'- agaCgCGUa-CCGCGGgCGCCUuuuuu -5'
miRNA: 3'- agaCGCG--UACCGCG---GGCGCCUUUUuu -5'
miRNA: 3'- aGACGCG----UACCGCGGGC-GCCUUuuuu -5'
miRNA: 3'- -AGACGCGUACCGCGGGCGCCUUUUUU- -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 | |||||||
| 3510 | 3' | -55.6 | NC_001623.1 | + | 55090 | 0.66 | 0.870852 |
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Target: 5'- --cGUuuGUGGCGCCgggCGUGGAAGGAAa -3' miRNA: 3'- agaCGcgUACCGCGG---GCGCCUUUUUU- -5' |
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| 3510 | 3' | -55.6 | NC_001623.1 | + | 55676 | 0.68 | 0.775485 |
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Target: 5'- --cGgGCAcgGGCGCCgGCGGAu---- -3' miRNA: 3'- agaCgCGUa-CCGCGGgCGCCUuuuuu -5' |
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| 3510 | 3' | -55.6 | NC_001623.1 | + | 113226 | 0.68 | 0.765816 |
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Target: 5'- --cGCGUacGUGGCGUuugCCGUGGAAAAc- -3' miRNA: 3'- agaCGCG--UACCGCG---GGCGCCUUUUuu -5' |
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| 3510 | 3' | -55.6 | NC_001623.1 | + | 38172 | 0.76 | 0.337581 |
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Target: 5'- aCUGCGUggacGUGGUGCCCGaCGGGAu--- -3' miRNA: 3'- aGACGCG----UACCGCGGGC-GCCUUuuuu -5' |
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| 3510 | 3' | -55.6 | NC_001623.1 | + | 101405 | 1.07 | 0.003075 |
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Target: 5'- gUCUGCGCAUGGCGCCCGCGGAAAAAAa -3' miRNA: 3'- -AGACGCGUACCGCGGGCGCCUUUUUU- -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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