miRNA: 3'- uaCCG---UCgCGUUCCUU-CCGG--UGguCG- -5'
miRNA: 3'- uaCCGuCGCGuUCCu---UCCGG---UGGUCG- -5'
miRNA: 3'- uaCCG----UCGCguucCUUCCGGUGGUCG- -5'
miRNA: 3'- -UACCGUCGCGUUCCUUCCGGUGGUCG- -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 | |||||||
| 2192 | 5' | -58.3 | NC_001396.1 | + | 1875 | 0.66 | 0.10097 |
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Target: 5'- -aGGCgauGGgGCAGGGGAuGGCCucGCguGCc -3' miRNA: 3'- uaCCG---UCgCGUUCCUU-CCGG--UGguCG- -5' |
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| 2192 | 5' | -58.3 | NC_001396.1 | + | 3817 | 0.69 | 0.055135 |
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Target: 5'- -aGGCuGUGCcAGGuuguAGGCCaugACCAGUg -3' miRNA: 3'- uaCCGuCGCGuUCCu---UCCGG---UGGUCG- -5' |
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| 2192 | 5' | -58.3 | NC_001396.1 | + | 5219 | 0.69 | 0.048113 |
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Target: 5'- -cGGCuaccGGCGa---GAGGGCCGCUAGCa -3' miRNA: 3'- uaCCG----UCGCguucCUUCCGGUGGUCG- -5' |
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| 2192 | 5' | -58.3 | NC_001396.1 | + | 1450 | 1.1 | 1.3e-05 |
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Target: 5'- aAUGGCAGCGCAAGGAAGGCCACCAGCa -3' miRNA: 3'- -UACCGUCGCGUUCCUUCCGGUGGUCG- -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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