miRNA: 3'- -UAGGcGUAACGa---CU-----ACUGGGaACGCC- -5'
miRNA: 3'- -UAGgCGUA--------------ACGACUACuGGGAACGcc -5'
miRNA: 3'- -UAGGCGUA--ACgACUA-CUGGGaaCGCC- -5'
miRNA: 3'- -UAGGCGUaaCGACuaCUGGGaa---CGCC- -5'
miRNA: 3'- -UAGgCGUaacGACUACUGGGA---ACGCC- -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 | |||||||
| 30856 | 5' | -53.6 | NC_006552.1 | + | 43855 | 0.68 | 0.730329 |
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Target: 5'- cAUCCaCAUUGCgcgcGAcuaacUGGCCCaUGCGGu -3' miRNA: 3'- -UAGGcGUAACGa---CU-----ACUGGGaACGCC- -5' |
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| 30856 | 5' | -53.6 | NC_006552.1 | + | 31145 | 0.68 | 0.705522 |
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Target: 5'- aGUCgGCAUucuucucgugcgggUGUUGAUG-CCCUUGCa- -3' miRNA: 3'- -UAGgCGUA--------------ACGACUACuGGGAACGcc -5' |
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| 30856 | 5' | -53.6 | NC_006552.1 | + | 42690 | 0.7 | 0.598248 |
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Target: 5'- gAUCUGCGUaaUGgUGAUaGGCCUggGCGGa -3' miRNA: 3'- -UAGGCGUA--ACgACUA-CUGGGaaCGCC- -5' |
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| 30856 | 5' | -53.6 | NC_006552.1 | + | 64485 | 0.71 | 0.511333 |
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Target: 5'- cAUCCGCAc-GCUGgcGGCCUggcagGCGGg -3' miRNA: 3'- -UAGGCGUaaCGACuaCUGGGaa---CGCC- -5' |
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| 30856 | 5' | -53.6 | NC_006552.1 | + | 9578 | 0.72 | 0.500804 |
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Target: 5'- uGUCgGCGaa-CUGAUGGCCCUggcUGCGGc -3' miRNA: 3'- -UAGgCGUaacGACUACUGGGA---ACGCC- -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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