miRNA: 3'- guCGAGU---ACUGCUAagUCUA--GGUCGU- -5'
miRNA: 3'- -GUCG----AGUaCUGCUAAGUCUa--GGUCGU- -5'
miRNA: 3'- gUCGAguacUGCUaAGUCUAGGUCGU- -5'
miRNA: 3'- -GUCGAGUa--CugCuaa-GUCUAGGUCGu -5'
miRNA: 3'- -GUCGAGUACUGCUAAGUCUAGGUCGU- -5'
Results 1 - 5 of 5 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 | |||||||
| 13546 | 5' | -50.4 | NC_003444.1 | + | 8863 | 0.66 | 0.838248 |
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Target: 5'- -cGCUCAagcUGACGGU--AGGUugCCAGCAg -3' miRNA: 3'- guCGAGU---ACUGCUAagUCUA--GGUCGU- -5' |
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| 13546 | 5' | -50.4 | NC_003444.1 | + | 8952 | 0.67 | 0.798371 |
|
Target: 5'- aCAGCguguUCA-GGCGGUUCGGAacgCUGGCAu -3' miRNA: 3'- -GUCG----AGUaCUGCUAAGUCUa--GGUCGU- -5' |
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| 13546 | 5' | -50.4 | NC_003444.1 | + | 10705 | 0.7 | 0.615611 |
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Target: 5'- uGGCU----ACGA-UCAGAUCCAGCAg -3' miRNA: 3'- gUCGAguacUGCUaAGUCUAGGUCGU- -5' |
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| 13546 | 5' | -50.4 | NC_003444.1 | + | 16277 | 0.73 | 0.466776 |
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Target: 5'- uCAGUUCAgugGugGugcgCGGAUCCAGCu -3' miRNA: 3'- -GUCGAGUa--CugCuaa-GUCUAGGUCGu -5' |
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| 13546 | 5' | -50.4 | NC_003444.1 | + | 7198 | 1.09 | 0.001669 |
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Target: 5'- uCAGCUCAUGACGAUUCAGAUCCAGCAg -3' miRNA: 3'- -GUCGAGUACUGCUAAGUCUAGGUCGU- -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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