miRNA: 3'- -UGGCC-GCAAG------------CCGAGuuAGUC--CCACU- -5'
miRNA: 3'- uGGCCGcaa---GCCGAGUU--AGUCCCACu -5'
miRNA: 3'- -UGG-CCGCa-AG---CCGAGUuaGUC-CCACU- -5'
miRNA: 3'- uGGCCGCaaGCCGAguuaGUCCCACU- -5'
miRNA: 3'- -UGGCCGCAAGCCGAGUUAGUCCCACU- -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 | |||||||
| 25989 | 5' | -56.1 | NC_005340.1 | + | 9875 | 0.66 | 0.501071 |
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Target: 5'- cGCCGGuCGUUCgcggacauggugGGCUCccUCGGucGGUGAg -3' miRNA: 3'- -UGGCC-GCAAG------------CCGAGuuAGUC--CCACU- -5' |
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| 25989 | 5' | -56.1 | NC_005340.1 | + | 11941 | 0.67 | 0.418532 |
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Target: 5'- cCCGGCacauucCGGCUUGAuaUCGGGGUGc -3' miRNA: 3'- uGGCCGcaa---GCCGAGUU--AGUCCCACu -5' |
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| 25989 | 5' | -56.1 | NC_005340.1 | + | 9197 | 0.67 | 0.408802 |
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Target: 5'- gACCgGGCGcgUCacuGGCUCAggCAGcGGUGGc -3' miRNA: 3'- -UGG-CCGCa-AG---CCGAGUuaGUC-CCACU- -5' |
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| 25989 | 5' | -56.1 | NC_005340.1 | + | 8197 | 0.68 | 0.362334 |
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Target: 5'- uCUGGCGcaCGGCUgg--CGGGGUGAu -3' miRNA: 3'- uGGCCGCaaGCCGAguuaGUCCCACU- -5' |
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| 25989 | 5' | -56.1 | NC_005340.1 | + | 16840 | 1.08 | 0.000453 |
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Target: 5'- uACCGGCGUUCGGCUCAAUCAGGGUGAc -3' miRNA: 3'- -UGGCCGCAAGCCGAGUUAGUCCCACU- -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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