miRNA: 3'- -AGUUGcaca-UGGGCACGCGUgGGCAG- -5'
miRNA: 3'- -AGUU-GCAcAUGGGCACGCGugg---GCAG- -5'
miRNA: 3'- aGUUGCACAUgGGCA--------------C-GCGUGGGCAG- -5'
miRNA: 3'- -AGUUGCACAUGGGCACGCGUGGGCAG- -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 | |||||||
| 719 | 5' | -56.1 | AC_000019.1 | + | 23067 | 0.66 | 0.550433 |
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Target: 5'- uUCAGCuacccGCCCGUGCGCA-UCGUUg -3' miRNA: 3'- -AGUUGcaca-UGGGCACGCGUgGGCAG- -5' |
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| 719 | 5' | -56.1 | AC_000019.1 | + | 9343 | 0.69 | 0.351398 |
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Target: 5'- aUCGAcCGUuUGCCCGUGCGCcgucgaCGUCg -3' miRNA: 3'- -AGUU-GCAcAUGGGCACGCGugg---GCAG- -5' |
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| 719 | 5' | -56.1 | AC_000019.1 | + | 15258 | 0.71 | 0.292555 |
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Target: 5'- cCAACGUGUGaCCGUuacugacgccagacGcCGCACCUGUCc -3' miRNA: 3'- aGUUGCACAUgGGCA--------------C-GCGUGGGCAG- -5' |
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| 719 | 5' | -56.1 | AC_000019.1 | + | 15908 | 1.09 | 0.000478 |
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Target: 5'- gUCAACGUGUACCCGUGCGCACCCGUCc -3' miRNA: 3'- -AGUUGCACAUGGGCACGCGUGGGCAG- -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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