miRNA: 3'- -GAUaGGAGCUA--AGUGAgagGCCGGUC- -5'
miRNA: 3'- gaUAGGAGCua----AGUGa--------GAGgCCGGUC- -5'
miRNA: 3'- gaUAGGA-------GCUAAGuGAGAGGCCGGuc -5'
miRNA: 3'- gaUAGGAGCUAAGUgAGA-GGCC----GGUC- -5'
miRNA: 3'- -GAUAGGAGCUAAGUGAGAGGCCGGUC- -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 | |||||||
| 22040 | 3' | -53.1 | NC_004927.1 | + | 58529 | 0.66 | 0.890262 |
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Target: 5'- gCUA-CCUCGAUgcUCGCUa--UGGCCGGu -3' miRNA: 3'- -GAUaGGAGCUA--AGUGAgagGCCGGUC- -5' |
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| 22040 | 3' | -53.1 | NC_004927.1 | + | 27802 | 0.68 | 0.7872 |
|
Target: 5'- -cGUCCUCGuuguagUCACcgcccugcgCUCgGGCCAGu -3' miRNA: 3'- gaUAGGAGCua----AGUGa--------GAGgCCGGUC- -5' |
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| 22040 | 3' | -53.1 | NC_004927.1 | + | 3884 | 0.71 | 0.649649 |
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Target: 5'- -cAUCCUcccaauaCGAUUC-CUCUCCGGCUu- -3' miRNA: 3'- gaUAGGA-------GCUAAGuGAGAGGCCGGuc -5' |
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| 22040 | 3' | -53.1 | NC_004927.1 | + | 4208 | 0.71 | 0.617986 |
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Target: 5'- -cAUCCUCGAUUCGgUCUuCCGGggcgUCGGg -3' miRNA: 3'- gaUAGGAGCUAAGUgAGA-GGCC----GGUC- -5' |
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| 22040 | 3' | -53.1 | NC_004927.1 | + | 16855 | 1.08 | 0.002855 |
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Target: 5'- gCUAUCCUCGAUUCACUCUCCGGCCAGc -3' miRNA: 3'- -GAUAGGAGCUAAGUGAGAGGCCGGUC- -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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