miRNA: 3'- gCUGaaGGcAGACGCGCCG-GAGCAGc -5'
miRNA: 3'- -GCUGa----AGGCa---Ga-----CGCGCCGGa-GCAGC- -5'
miRNA: 3'- gCUGaaGGCAG--ACGC--GCCGGAGCAGC- -5'
miRNA: 3'- -GCUGAAGGCAGACGCGCCGGAGCAGC- -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 | |||||||
| 7310 | 5' | -58.2 | NC_001900.1 | + | 36236 | 0.68 | 0.442503 |
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Target: 5'- uGAUcgCC-UCUGCGUGGCgCUCGUUc -3' miRNA: 3'- gCUGaaGGcAGACGCGCCG-GAGCAGc -5' |
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| 7310 | 5' | -58.2 | NC_001900.1 | + | 25834 | 0.68 | 0.433038 |
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Target: 5'- aCGAUgaagcUCCGcgugCgccgggGCGCGGCCcgCGUCGg -3' miRNA: 3'- -GCUGa----AGGCa---Ga-----CGCGCCGGa-GCAGC- -5' |
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| 7310 | 5' | -58.2 | NC_001900.1 | + | 28217 | 0.7 | 0.337288 |
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Target: 5'- uGGCc-UCGUCcuUGCGgaCGGCCUCGUCGg -3' miRNA: 3'- gCUGaaGGCAG--ACGC--GCCGGAGCAGC- -5' |
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| 7310 | 5' | -58.2 | NC_001900.1 | + | 20153 | 1.08 | 0.000662 |
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Target: 5'- gCGACUUCCGUCUGCGCGGCCUCGUCGc -3' miRNA: 3'- -GCUGAAGGCAGACGCGCCGGAGCAGC- -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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