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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 | |||||||
| 12099 | 3' | -56 | NC_003309.1 | + | 2663 | 1.05 | 0.001321 |
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Target: 5'- gCUCUCCGCAAGCAGCGUCACGCAGUUu -3' miRNA: 3'- -GAGAGGCGUUCGUCGCAGUGCGUCAA- -5' |
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| 12099 | 3' | -56 | NC_003309.1 | + | 47789 | 0.7 | 0.363356 |
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Target: 5'- gUCUCauucccgaaGCGGGCAGCcUCGCGCAGc- -3' miRNA: 3'- gAGAGg--------CGUUCGUCGcAGUGCGUCaa -5' |
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| 12099 | 3' | -56 | NC_003309.1 | + | 7368 | 0.7 | 0.390208 |
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Target: 5'- -cCUUCGCAccAGcCAGCGUCGCGCGc-- -3' miRNA: 3'- gaGAGGCGU--UC-GUCGCAGUGCGUcaa -5' |
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| 12099 | 3' | -56 | NC_003309.1 | + | 19463 | 0.69 | 0.447638 |
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Target: 5'- aUCUCCGUucGCuGCGUguCGCGGc- -3' miRNA: 3'- gAGAGGCGuuCGuCGCAguGCGUCaa -5' |
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| 12099 | 3' | -56 | NC_003309.1 | + | 3479 | 0.67 | 0.530868 |
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Target: 5'- -gCUCCGC-GGCAGCaaaagGUCGCGCGu-- -3' miRNA: 3'- gaGAGGCGuUCGUCG-----CAGUGCGUcaa -5' |
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| 12099 | 3' | -56 | NC_003309.1 | + | 46174 | 0.67 | 0.57458 |
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Target: 5'- -gUUCCGCcucaaCAGCGUCACGCAc-- -3' miRNA: 3'- gaGAGGCGuuc--GUCGCAGUGCGUcaa -5' |
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| 12099 | 3' | -56 | NC_003309.1 | + | 27122 | 0.66 | 0.585651 |
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Target: 5'- gCUUUCCGCucGCAcGCG-C-CGCAGUg -3' miRNA: 3'- -GAGAGGCGuuCGU-CGCaGuGCGUCAa -5' |
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| 12099 | 3' | -56 | NC_003309.1 | + | 27959 | 0.66 | 0.619065 |
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Target: 5'- -gCUCCGCAGuuGCAucgcagauGCGUCGCgGCGGg- -3' miRNA: 3'- gaGAGGCGUU--CGU--------CGCAGUG-CGUCaa -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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