miRNA: 3'- cGUCaAAGCUCCCGCACG-GgGa----ACUc -5'
miRNA: 3'- -CGUCAAA------------GCUcCCGCaCGGGGAACUC- -5'
miRNA: 3'- -CGUCaa----AGCU-CCCGCACGgGG----AACUC- -5'
miRNA: 3'- -CGUCAAAGCUCCCGCACGGGGAACUC- -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 | |||||||
| 7674 | 3' | -55.3 | NC_001973.1 | + | 120783 | 0.66 | 0.938488 |
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Target: 5'- cCGGcUUCGAGGGCGUGCgCgCgcugcUGAc -3' miRNA: 3'- cGUCaAAGCUCCCGCACG-GgGa----ACUc -5' |
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| 7674 | 3' | -55.3 | NC_001973.1 | + | 109109 | 0.66 | 0.938488 |
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Target: 5'- uGCGGUUUguugaaccgccgCGGcGGCG-GCCUCUUGGGc -3' miRNA: 3'- -CGUCAAA------------GCUcCCGCaCGGGGAACUC- -5' |
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| 7674 | 3' | -55.3 | NC_001973.1 | + | 81044 | 0.68 | 0.840548 |
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Target: 5'- uGCGGgccgcgUCGAcGGGCGUGCgCUucagUUGGGa -3' miRNA: 3'- -CGUCaa----AGCU-CCCGCACGgGG----AACUC- -5' |
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| 7674 | 3' | -55.3 | NC_001973.1 | + | 131181 | 1.1 | 0.003194 |
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Target: 5'- uGCAGUUUCGAGGGCGUGCCCCUUGAGc -3' miRNA: 3'- -CGUCAAAGCUCCCGCACGGGGAACUC- -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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