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miRNA: 3'- cUCCACaa-------GGGCCuCGACAAGgGUGu -5'
miRNA: 3'- -CUC-CACAAGGGCC--------------UCGACAAGGGUGU- -5'
miRNA: 3'- cUCCACA-----------AGGGCCUCGAC---------AAGGGugu -5'
miRNA: 3'- -CUCCACAAGGGCCUCGACAAGGGUGU- -5'
Results 1 - 4 of 4 are showing below:
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| ID | Location | Perfect MFE.* | RefSeq Acc. | strand | Start Position |
R_P_ratio#
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P value |
| Predicted miRNA align pattern | |||||||
| 7222 | 3' | -56.4 | NC_001900.1 | + | 9403 | 0.67 | 0.54384 |
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Target: 5'- cAGGUGccggaugaaCCCGGuGCUGUUCgCGCu -3' miRNA: 3'- cUCCACaa-------GGGCCuCGACAAGgGUGu -5' |
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| 7222 | 3' | -56.4 | NC_001900.1 | + | 19102 | 0.68 | 0.477499 |
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Target: 5'- aGGGcGUGUUCCUGGccacagacguggagGGUUGUUUCUACGa -3' miRNA: 3'- -CUC-CACAAGGGCC--------------UCGACAAGGGUGU- -5' |
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| 7222 | 3' | -56.4 | NC_001900.1 | + | 32133 | 0.7 | 0.357656 |
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Target: 5'- uAGGUGUugggagcgaucUCCCGGAGCUGccgaagcaaUUCCCc-- -3' miRNA: 3'- cUCCACA-----------AGGGCCUCGAC---------AAGGGugu -5' |
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| 7222 | 3' | -56.4 | NC_001900.1 | + | 13233 | 1.08 | 0.000698 |
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Target: 5'- cGAGGUGUUCCCGGAGCUGUUCCCACAc -3' miRNA: 3'- -CUCCACAAGGGCCUCGACAAGGGUGU- -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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