miRNA: 3'- gcaAGGGCUAUCGG-----UGGG----CUACUuuu -5'
miRNA: 3'- -GCaaGGGCua-UCGGUGGGCUAcuuuu -5'
miRNA: 3'- -GCAAGGGCUAUCGGUGGGCUACUUUU- -5'
miRNA: 3'- -GCaAGGGCUAU------CGGUGGGCUaCUUUu -5'
miRNA: 3'- -GCaaGGGCUA--UCGG----UGGG-CUACUUUu -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 |
| Predicted miRNA align pattern | |||||||
| 12359 | 3' | -51.7 | NC_003324.1 | + | 27526 | 0.66 | 0.894646 |
|
Target: 5'- --aUCCCGAUAGCCccguuGCCUaucaGAUGGc-- -3' miRNA: 3'- gcaAGGGCUAUCGG-----UGGG----CUACUuuu -5' |
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| 12359 | 3' | -51.7 | NC_003324.1 | + | 49322 | 0.68 | 0.808749 |
|
Target: 5'- aCGggCCCGucgGGCUGCCCGAUc---- -3' miRNA: 3'- -GCaaGGGCua-UCGGUGGGCUAcuuuu -5' |
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| 12359 | 3' | -51.7 | NC_003324.1 | + | 27254 | 1.07 | 0.003192 |
|
Target: 5'- gCGUUCCCGAUAGCCACCCGAUGAAAAg -3' miRNA: 3'- -GCAAGGGCUAUCGGUGGGCUACUUUU- -5' |
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| 12359 | 3' | -51.7 | NC_003324.1 | + | 51102 | 0.69 | 0.747213 |
|
Target: 5'- aCGgUCCCGAUGuaccucGUCACCCGA-GAGGg -3' miRNA: 3'- -GCaAGGGCUAU------CGGUGGGCUaCUUUu -5' |
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| 12359 | 3' | -51.7 | NC_003324.1 | + | 20209 | 0.69 | 0.75785 |
|
Target: 5'- aCGcgCCCGGUauGGCCggcaGCCCaGAUGGAAu -3' miRNA: 3'- -GCaaGGGCUA--UCGG----UGGG-CUACUUUu -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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