miRNA: 3'- caAGUGCCCaca-GUCAAGcAGcAGCG- -5'
miRNA: 3'- caagUGCCCaCa-GUCA-AGCA-GCAGCG- -5'
miRNA: 3'- caAGUGCCCACaGUCaa-----GCAGC--AGCG- -5'
miRNA: 3'- -CAAGUGCCCAca---GUC---AAGC-AGCAGCG- -5'
miRNA: 3'- -CAAGUGCCCACAGUCAAGCAGCAGCG- -5'
Results 1 - 5 of 5 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 | |||||||
| 27991 | 5' | -52 | NC_005886.2 | + | 23902 | 0.66 | 0.877331 |
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Target: 5'- -gUCACGGGgcagCGGUUC-UCaUCGCu -3' miRNA: 3'- caAGUGCCCaca-GUCAAGcAGcAGCG- -5' |
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| 27991 | 5' | -52 | NC_005886.2 | + | 35507 | 0.66 | 0.843816 |
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Target: 5'- ---aACGGGcGcgCAGUaUCGUgCGUCGCg -3' miRNA: 3'- caagUGCCCaCa-GUCA-AGCA-GCAGCG- -5' |
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| 27991 | 5' | -52 | NC_005886.2 | + | 1054 | 0.66 | 0.843816 |
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Target: 5'- -gUCGCGGGUG-CAGaaacggaUGUCGaaUCGCu -3' miRNA: 3'- caAGUGCCCACaGUCaa-----GCAGC--AGCG- -5' |
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| 27991 | 5' | -52 | NC_005886.2 | + | 25883 | 0.72 | 0.556592 |
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Target: 5'- aGUUCGCGGGUuugcgCGGccaUUCGuUCGUCGUg -3' miRNA: 3'- -CAAGUGCCCAca---GUC---AAGC-AGCAGCG- -5' |
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| 27991 | 5' | -52 | NC_005886.2 | + | 41249 | 1.13 | 0.001171 |
|
Target: 5'- uGUUCACGGGUGUCAGUUCGUCGUCGCa -3' miRNA: 3'- -CAAGUGCCCACAGUCAAGCAGCAGCG- -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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