miRNA: 3'- uuuUUCGCC-CuuUAAC-----UCCGUACCGC- -5'
miRNA: 3'- -UUUUUCG--------CCCUuu--AACUCCGUACCGc -5'
miRNA: 3'- uuUUUCGCCcuuUAACUCCGuaCCGC- -5'
miRNA: 3'- -UUUUUCGCCCUUUAACUCCGUACCGC- -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 | |||||||
| 12754 | 5' | -49.3 | NC_003356.1 | + | 39444 | 0.69 | 0.777267 |
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Target: 5'- --uGGGCGGuGccAUUGguauuGGGCGUGGCGg -3' miRNA: 3'- uuuUUCGCC-CuuUAAC-----UCCGUACCGC- -5' |
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| 12754 | 5' | -49.3 | NC_003356.1 | + | 42363 | 0.69 | 0.755245 |
|
Target: 5'- cAAAAAGUucugcuucGGGAcguuUUGGGGCAUGGUu -3' miRNA: 3'- -UUUUUCG--------CCCUuu--AACUCCGUACCGc -5' |
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| 12754 | 5' | -49.3 | NC_003356.1 | + | 23788 | 0.77 | 0.328004 |
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Target: 5'- -uGAGGCGGcu-AUUGAGGCcgGGCGu -3' miRNA: 3'- uuUUUCGCCcuuUAACUCCGuaCCGC- -5' |
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| 12754 | 5' | -49.3 | NC_003356.1 | + | 41861 | 1.07 | 0.00338 |
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Target: 5'- cAAAAAGCGGGAAAUUGAGGCAUGGCGu -3' miRNA: 3'- -UUUUUCGCCCUUUAACUCCGUACCGC- -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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