miRNA: 3'- guaGCGGUCuCCACUgUGguGCCGCG- -5'
miRNA: 3'- -GUagCGGUCUCCACUGUgGU---GCCGCG- -5'
miRNA: 3'- guAGCGGuCUCCaCUG--------UGGU---GCCGCG- -5'
miRNA: 3'- -GUAGCGGUCUCCACUGUGGUGCCGCG- -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 | |||||||
| 32013 | 5' | -57.4 | NC_006949.1 | + | 18177 | 0.66 | 0.572645 |
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Target: 5'- --cCGUCAGuGGUGGgACacUGGCGCa -3' miRNA: 3'- guaGCGGUCuCCACUgUGguGCCGCG- -5' |
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| 32013 | 5' | -57.4 | NC_006949.1 | + | 16480 | 0.69 | 0.365452 |
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Target: 5'- aUAagGCCGGAGGUGGCGgUGgggUGGUGCa -3' miRNA: 3'- -GUagCGGUCUCCACUGUgGU---GCCGCG- -5' |
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| 32013 | 5' | -57.4 | NC_006949.1 | + | 4768 | 0.7 | 0.348541 |
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Target: 5'- -cUCGCCuGAGGgGAUuaacgcagGCCAuauCGGCGCg -3' miRNA: 3'- guAGCGGuCUCCaCUG--------UGGU---GCCGCG- -5' |
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| 32013 | 5' | -57.4 | NC_006949.1 | + | 8413 | 1.11 | 0.000358 |
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Target: 5'- aCAUCGCCAGAGGUGACACCACGGCGCu -3' miRNA: 3'- -GUAGCGGUCUCCACUGUGGUGCCGCG- -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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