miRNA: 3'- aCAUC-CGAUUUUA-------GGGuAGCGGGaac -5'
miRNA: 3'- aCAU--CCgaUUUUAGGGUAGCGGGaac -5'
miRNA: 3'- -ACAUCCGAUUUUAGGGUAGCGGGAAC- -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 | |||||||
| 28225 | 3' | -49.8 | NC_005891.1 | + | 7322 | 0.67 | 0.815503 |
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Target: 5'- gGUGGaGCUGGAAUguucacgCCC-UCGCCCa-- -3' miRNA: 3'- aCAUC-CGAUUUUA-------GGGuAGCGGGaac -5' |
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| 28225 | 3' | -49.8 | NC_005891.1 | + | 12770 | 0.68 | 0.77476 |
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Target: 5'- cGUAcuGGagAAAAUCCCGUCGCCUc-- -3' miRNA: 3'- aCAU--CCgaUUUUAGGGUAGCGGGaac -5' |
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| 28225 | 3' | -49.8 | NC_005891.1 | + | 33603 | 1.08 | 0.002371 |
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Target: 5'- cUGUAGGCUAAAAUCCCAUCGCCCUUGc -3' miRNA: 3'- -ACAUCCGAUUUUAGGGUAGCGGGAAC- -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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