miRNA: 3'- gaCGUCAGCU---UGU---------------UCCCGUCUAgaua -5'
miRNA: 3'- gaCGUCAGCUUGUUC---CCGUCUaGAUA- -5'
miRNA: 3'- -GACGUCAGCUUGUUCCCGUCUAGAUA- -5'
Results 1 - 3 of 3 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 | |||||||
| 21192 | 5' | -51.2 | NC_004778.3 | + | 94195 | 0.66 | 0.974446 |
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Target: 5'- -cGCAGUCGGugcACAggcacgaguggccgcAGGGCAGGUa--- -3' miRNA: 3'- gaCGUCAGCU---UGU---------------UCCCGUCUAgaua -5' |
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| 21192 | 5' | -51.2 | NC_004778.3 | + | 29137 | 0.7 | 0.880945 |
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Target: 5'- -cGCGGUUGGACAGGcguGGCGGG-CUAUg -3' miRNA: 3'- gaCGUCAGCUUGUUC---CCGUCUaGAUA- -5' |
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| 21192 | 5' | -51.2 | NC_004778.3 | + | 115478 | 1.06 | 0.009458 |
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Target: 5'- gCUGCAGUCGAACAAGGGCAGAUCUAUu -3' miRNA: 3'- -GACGUCAGCUUGUUCCCGUCUAGAUA- -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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