miRNA: 3'- ucaCUGGUU---UUGGgaUUUUUGUCCCc -5'
miRNA: 3'- ucACUgg--UUUUGGGa---UUUUUGUCCCc -5'
miRNA: 3'- -UCAcugGUuUUGGGaUUUUUGUCCCC- -5'
miRNA: 3'- uCACUGGUuuuGGGA---UUUUUGUC---CCC- -5'
miRNA: 3'- -UCACUGGUUUUGGGAUUUUUGUCCCC- -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 | |||||||
| 4401 | 5' | -46.3 | NC_001724.1 | + | 1059 | 0.66 | 0.775338 |
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Target: 5'- --aGAUCAAaagGACCgaAGAAACGGGGc -3' miRNA: 3'- ucaCUGGUU---UUGGgaUUUUUGUCCCc -5' |
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| 4401 | 5' | -46.3 | NC_001724.1 | + | 1563 | 0.66 | 0.738181 |
|
Target: 5'- -aUGAagcaGGGACCCggagGAGGACAGGGu -3' miRNA: 3'- ucACUgg--UUUUGGGa---UUUUUGUCCCc -5' |
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| 4401 | 5' | -46.3 | NC_001724.1 | + | 9208 | 0.69 | 0.567731 |
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Target: 5'- aGGUcuaCGuGACCC-AGAGACAGGGGa -3' miRNA: 3'- -UCAcugGUuUUGGGaUUUUUGUCCCC- -5' |
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| 4401 | 5' | -46.3 | NC_001724.1 | + | 2251 | 0.7 | 0.541762 |
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Target: 5'- uGUGGCCGu--CCCUucaAGGAGCAGaguGGGg -3' miRNA: 3'- uCACUGGUuuuGGGA---UUUUUGUC---CCC- -5' |
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| 4401 | 5' | -46.3 | NC_001724.1 | + | 7724 | 1.12 | 0.000643 |
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Target: 5'- gAGUGACCAAAACCCUAAAAACAGGGGu -3' miRNA: 3'- -UCACUGGUUUUGGGAUUUUUGUCCCC- -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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