miRNA: 3'- ccgACACGAAGA---------------AGGUCGAUCcCGac -5'
miRNA: 3'- cCGACACGAAGaa---GgUCGA-----UCC-CGAC- -5'
miRNA: 3'- -CCGACACGAAGAAGGUCGAUCCCGAC- -5'
Results 1 - 3 of 3 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 | |||||||
| 9398 | 5' | -54.9 | NC_002513.1 | + | 32611 | 0.66 | 0.556674 |
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Target: 5'- --gUGUGCUUCUacuuauguuagaaguUCCAGCUGGaGCa- -3' miRNA: 3'- ccgACACGAAGA---------------AGGUCGAUCcCGac -5' |
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| 9398 | 5' | -54.9 | NC_002513.1 | + | 32659 | 0.67 | 0.485451 |
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Target: 5'- uGCUGUGCUUCcuaagCgAGCUucugcAGGaGCUGc -3' miRNA: 3'- cCGACACGAAGaa---GgUCGA-----UCC-CGAC- -5' |
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| 9398 | 5' | -54.9 | NC_002513.1 | + | 14981 | 1.1 | 0.000348 |
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Target: 5'- cGGCUGUGCUUCUUCCAGCUAGGGCUGu -3' miRNA: 3'- -CCGACACGAAGAAGGUCGAUCCCGAC- -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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