miRNA: 3'- uuUCGCCCC-GCUGCUgg-UCGGCCGCa -5'
miRNA: 3'- -UUUCGcCCCGCUG-CUgGUCGg--CCGca -5'
miRNA: 3'- uuucgCCCCGCUGCUGGuc-GGCCGCa -5'
miRNA: 3'- -UUUCGCCCCGCUGCUGGUCGGCCGCA- -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 | |||||||
| 9812 | 5' | -62.6 | NC_002593.1 | + | 57703 | 0.67 | 0.438507 |
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Target: 5'- -cGGUGGGGuCGGCGGuggGGUCGGCGg -3' miRNA: 3'- uuUCGCCCC-GCUGCUgg-UCGGCCGCa -5' |
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| 9812 | 5' | -62.6 | NC_002593.1 | + | 62335 | 0.67 | 0.420831 |
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Target: 5'- aAAGGCaGGGCGGCuGAgCAGCagaGGCa- -3' miRNA: 3'- -UUUCGcCCCGCUG-CUgGUCGg--CCGca -5' |
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| 9812 | 5' | -62.6 | NC_002593.1 | + | 18033 | 0.71 | 0.239625 |
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Target: 5'- ----gGGGGUGGCGACCucaCCGGCGa -3' miRNA: 3'- uuucgCCCCGCUGCUGGuc-GGCCGCa -5' |
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| 9812 | 5' | -62.6 | NC_002593.1 | + | 70217 | 1.04 | 0.000956 |
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Target: 5'- aAAAGCGGGGCGACGACCAGCCGGCGUc -3' miRNA: 3'- -UUUCGCCCCGCUGCUGGUCGGCCGCA- -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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