miRNA: 3'- -ACUU--------------UCUCGCGC---AGUUCC--GGCGCGac -5'
miRNA: 3'- aCUUUC----UCGCGCAGUUccggCGCGAC- -5'
miRNA: 3'- aCUUucucgCGCAGuuCCGGCGCGAC- -5'
miRNA: 3'- aCUUucuCGCGCAGUuc-CGGCGCGac -5'
miRNA: 3'- -ACUUUCUCGCGCAGUUCCGGCGCGAC- -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 | |||||||
| 12159 | 5' | -56.1 | NC_003309.1 | + | 34398 | 0.65 | 0.661245 |
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Target: 5'- gUGAAcgcaucaaagccuuGGAGCGCGaggUCAAGGaaCUGCGCc- -3' miRNA: 3'- -ACUU--------------UCUCGCGC---AGUUCC--GGCGCGac -5' |
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| 12159 | 5' | -56.1 | NC_003309.1 | + | 3305 | 0.66 | 0.653506 |
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Target: 5'- gGAAAGgcgcAGCGCGUCGAuca-GCGCUGc -3' miRNA: 3'- aCUUUC----UCGCGCAGUUccggCGCGAC- -5' |
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| 12159 | 5' | -56.1 | NC_003309.1 | + | 6042 | 0.66 | 0.653506 |
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Target: 5'- cGAAuca--GCGUCu-GGUCGCGCUGg -3' miRNA: 3'- aCUUucucgCGCAGuuCCGGCGCGAC- -5' |
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| 12159 | 5' | -56.1 | NC_003309.1 | + | 11231 | 0.68 | 0.511523 |
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Target: 5'- cGGAcu-GCGCGUCGucuGCCGCGCg- -3' miRNA: 3'- aCUUucuCGCGCAGUuc-CGGCGCGac -5' |
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| 12159 | 5' | -56.1 | NC_003309.1 | + | 36450 | 1.08 | 0.000893 |
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Target: 5'- uUGAAAGAGCGCGUCAAGGCCGCGCUGc -3' miRNA: 3'- -ACUUUCUCGCGCAGUUCCGGCGCGAC- -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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