miRNA: 3'- -CAGaCCGUCGGauuCGAUGUuuuuau -5'
miRNA: 3'- -CAGac-CGUCGG-----AUUCGAUGUUUUUau -5'
miRNA: 3'- caGACCGUCGGauuCGAUGuuuuuau -5'
miRNA: 3'- -CAGACCGUCGGAUUCGAUGUUUUUAU- -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 | |||||||
| 32025 | 3' | -46.8 | NC_006949.1 | + | 16164 | 0.66 | 0.97763 |
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Target: 5'- gGUCaGGCAGCUgccGCUGCAu----- -3' miRNA: 3'- -CAGaCCGUCGGauuCGAUGUuuuuau -5' |
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| 32025 | 3' | -46.8 | NC_006949.1 | + | 28680 | 0.67 | 0.945755 |
|
Target: 5'- uGUUgcaGCAGCCcugugUGAGCUACAGGAAc- -3' miRNA: 3'- -CAGac-CGUCGG-----AUUCGAUGUUUUUau -5' |
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| 32025 | 3' | -46.8 | NC_006949.1 | + | 10399 | 0.68 | 0.928508 |
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Target: 5'- -gCUGGCAGCCgacGCUGCc------ -3' miRNA: 3'- caGACCGUCGGauuCGAUGuuuuuau -5' |
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| 32025 | 3' | -46.8 | NC_006949.1 | + | 46424 | 1.08 | 0.004817 |
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Target: 5'- cGUCUGGCAGCCUAAGCUACAAAAAUAg -3' miRNA: 3'- -CAGACCGUCGGAUUCGAUGUUUUUAU- -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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