miRNA: 3'- -CGUU-GCGGAGCUA-GcAgCACUAGUUu -5'
miRNA: 3'- -CGUUgCGGAGCUaGCAGC-ACUAGUuu -5'
miRNA: 3'- -CGUUGCGGAG-------------CUAGCAGC--ACuaGUUU- -5'
miRNA: 3'- -CGUUGCGGAGCUAGCAGCACUAGUUU- -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 | |||||||
| 16695 | 5' | -50.1 | NC_004156.1 | + | 13701 | 0.66 | 0.998773 |
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Target: 5'- cGUAGuCGCCUCGGUgCuUgGUGGUCAGc -3' miRNA: 3'- -CGUU-GCGGAGCUA-GcAgCACUAGUUu -5' |
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| 16695 | 5' | -50.1 | NC_004156.1 | + | 190755 | 0.66 | 0.998773 |
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Target: 5'- aGCGAgGUCUUGA-CGUUGuUGAUCAu- -3' miRNA: 3'- -CGUUgCGGAGCUaGCAGC-ACUAGUuu -5' |
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| 16695 | 5' | -50.1 | NC_004156.1 | + | 197129 | 0.67 | 0.998494 |
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Target: 5'- uGUAACGCCUCccaaaguguacaaGAUUGUCGgcUGcgCAGAc -3' miRNA: 3'- -CGUUGCGGAG-------------CUAGCAGC--ACuaGUUU- -5' |
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| 16695 | 5' | -50.1 | NC_004156.1 | + | 180308 | 1.08 | 0.017633 |
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Target: 5'- gGCAACGCCUCGAUCGUCGUGAUCAAAc -3' miRNA: 3'- -CGUUGCGGAGCUAGCAGCACUAGUUU- -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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