miRNA: 3'- -CACCACCAUUUACGGACGUAGUGGGC- -5'
miRNA: 3'- cACC------------ACCaUUUACGGA---------------CGUAGUGGGC- -5'
miRNA: 3'- caCCACCAUUu--ACGgACG---UAGUGGgc -5'
miRNA: 3'- caccaCCAUUUAC-GGACGUaGUGGGC- -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# |
P value
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| Predicted miRNA align pattern | |||||||
| 1070 | 3' | -52.8 | NC_000929.1 | + | 29149 | 1.1 | 0.000746 |
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Target: 5'- cGUGGUGGUAAAUGCCUGCAUCACCCGg -3' miRNA: 3'- -CACCACCAUUUACGGACGUAGUGGGC- -5' |
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| 1070 | 3' | -52.8 | NC_000929.1 | + | 23211 | 0.68 | 0.562822 |
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Target: 5'- aUGGagcuugaaucaaUGGaAGGUGCCUccuucacgccuuccgGCAUCACCCGu -3' miRNA: 3'- cACC------------ACCaUUUACGGA---------------CGUAGUGGGC- -5' |
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| 1070 | 3' | -52.8 | NC_000929.1 | + | 17684 | 0.67 | 0.662573 |
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Target: 5'- -cGGUGGUAAuacUGCgUGCcagAUCGCCa- -3' miRNA: 3'- caCCACCAUUu--ACGgACG---UAGUGGgc -5' |
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| 1070 | 3' | -52.8 | NC_000929.1 | + | 20522 | 0.66 | 0.708614 |
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Target: 5'- ----cGGUAAAUGaCCUGUG-CGCCCGc -3' miRNA: 3'- caccaCCAUUUAC-GGACGUaGUGGGC- -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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