miRNA: 3'- aucAUCGGCucauGUGGCa-----AGGGCCU- -5'
miRNA: 3'- aucAUCGGCuCa---UGUGGCa--AGGGCCU- -5'
miRNA: 3'- -AUCAU---------CGGCUCa--UGuGGCaaGGGCCU- -5'
miRNA: 3'- aUCAUCGGCUCAUGUGGcaaGGgc-CU- -5'
miRNA: 3'- aUCA---UCGGCUCaUGuGGCaaGGGCCU- -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 | |||||||
| 2780 | 3' | -55.1 | NC_001491.2 | + | 49485 | 0.66 | 0.936953 |
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Target: 5'- --aUGGCCGuugcCGCCGgggccgUCCCGGAc -3' miRNA: 3'- aucAUCGGCucauGUGGCa-----AGGGCCU- -5' |
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| 2780 | 3' | -55.1 | NC_001491.2 | + | 40521 | 0.68 | 0.828626 |
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Target: 5'- --aUAGCCGcGcgcaGCACCGaggUCCCGGAg -3' miRNA: 3'- aucAUCGGCuCa---UGUGGCa--AGGGCCU- -5' |
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| 2780 | 3' | -55.1 | NC_001491.2 | + | 116341 | 0.68 | 0.828626 |
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Target: 5'- cUGGUGcgcuacaacGCCGAGgggGC-CCGggCCCGGGc -3' miRNA: 3'- -AUCAU---------CGGCUCa--UGuGGCaaGGGCCU- -5' |
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| 2780 | 3' | -55.1 | NC_001491.2 | + | 94116 | 0.7 | 0.765255 |
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Target: 5'- cGGUGGCCGGGUGCACCcggCCaacGAc -3' miRNA: 3'- aUCAUCGGCUCAUGUGGcaaGGgc-CU- -5' |
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| 2780 | 3' | -55.1 | NC_001491.2 | + | 146906 | 0.7 | 0.726195 |
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Target: 5'- cGGUccaGGCCGAG-GC-CCGggCCCGGGc -3' miRNA: 3'- aUCA---UCGGCUCaUGuGGCaaGGGCCU- -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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