miRNA: 3'- aCCUCUUCaGGuACCACGau--CGACCc -5'
miRNA: 3'- -ACC-UCUuca-GGU----AC-CACGAUCGACCC- -5'
miRNA: 3'- aCCUCUUCAGGuACCaCGa--UCGACCC- -5'
miRNA: 3'- -ACCUCUUCAGGUACCACGAUCGACCC- -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 | |||||||
| 11228 | 3' | -54.1 | NC_003043.1 | + | 7067 | 0.66 | 0.405363 |
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Target: 5'- gGGGGAAG-CC-UGGUGUcaccGCUGGu -3' miRNA: 3'- aCCUCUUCaGGuACCACGau--CGACCc -5' |
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| 11228 | 3' | -54.1 | NC_003043.1 | + | 1816 | 0.71 | 0.19678 |
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Target: 5'- aUGGcAGAuuugCCAacagUGuGUGCUGGCUGGGu -3' miRNA: 3'- -ACC-UCUuca-GGU----AC-CACGAUCGACCC- -5' |
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| 11228 | 3' | -54.1 | NC_003043.1 | + | 1635 | 0.78 | 0.062086 |
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Target: 5'- gGGGGAAGUUCcUGGcGCgcgGGCUGGGc -3' miRNA: 3'- aCCUCUUCAGGuACCaCGa--UCGACCC- -5' |
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| 11228 | 3' | -54.1 | NC_003043.1 | + | 1714 | 1.1 | 0.000173 |
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Target: 5'- uUGGAGAAGUCCAUGGUGCUAGCUGGGu -3' miRNA: 3'- -ACCUCUUCAGGUACCACGAUCGACCC- -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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