miRNA: 3'- -UUGuaGUUGCG---UCAGGuUUUGGGUGU- -5'
miRNA: 3'- -UUGuaGUUGCG---UCAGGuUUUGGGUGU- -5'
miRNA: 3'- -UUGUAGUUGCGUCaGGU--UUUGGg-UGU- -5'
miRNA: 3'- -UUGUAGUUGCGUCAGGUUUUGGGUGU- -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 | |||||||
| 31472 | 3' | -49.1 | NC_006650.1 | + | 18397 | 0.68 | 0.580322 |
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Target: 5'- aAACcgCAACGCccgAGUUCcGAACCUACGu -3' miRNA: 3'- -UUGuaGUUGCG---UCAGGuUUUGGGUGU- -5' |
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| 31472 | 3' | -49.1 | NC_006650.1 | + | 11875 | 0.68 | 0.580322 |
|
Target: 5'- aAACcgCAACGCccgAGUUCcGAACCUACGu -3' miRNA: 3'- -UUGuaGUUGCG---UCAGGuUUUGGGUGU- -5' |
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| 31472 | 3' | -49.1 | NC_006650.1 | + | 3710 | 0.71 | 0.425946 |
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Target: 5'- gAACGUCAACGCAGcCCAguAGACUaaACAg -3' miRNA: 3'- -UUGUAGUUGCGUCaGGU--UUUGGg-UGU- -5' |
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| 31472 | 3' | -49.1 | NC_006650.1 | + | 3628 | 1.07 | 0.00113 |
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Target: 5'- gAACAUCAACGCAGUCCAAAACCCACAa -3' miRNA: 3'- -UUGUAGUUGCGUCAGGUUUUGGGUGU- -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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