miRNA: 3'- -AUAGGUUUCGGUGUAAUUCGGAGAGG- -5'
miRNA: 3'- auAGGuuUCGGUGuaa----UUCG-GAGAGG- -5'
miRNA: 3'- auAGGuuUCGGUGuaa----UUCG-GAGAGG- -5'
miRNA: 3'- auAGGUUu------CGGuGUAAU-----UCGG-AGAGG- -5'
miRNA: 3'- auaGGUUUCGGUGUaa-UUCGGAGAGg -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 | |||||||
| 12309 | 3' | -48.1 | NC_003323.1 | + | 1599 | 1.13 | 0.000205 |
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Target: 5'- uUAUCCAAAGCCACAUUAAGCCUCUCCa -3' miRNA: 3'- -AUAGGUUUCGGUGUAAUUCGGAGAGG- -5' |
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| 12309 | 3' | -48.1 | NC_003323.1 | + | 442 | 0.68 | 0.412013 |
|
Target: 5'- -cUCCcuGGCCGCuccccugGAGCuCUCUCUc -3' miRNA: 3'- auAGGuuUCGGUGuaa----UUCG-GAGAGG- -5' |
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| 12309 | 3' | -48.1 | NC_003323.1 | + | 8658 | 0.68 | 0.412013 |
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Target: 5'- -cUCCcuGGCCGCuccccugGAGCuCUCUCUc -3' miRNA: 3'- auAGGuuUCGGUGuaa----UUCG-GAGAGG- -5' |
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| 12309 | 3' | -48.1 | NC_003323.1 | + | 4473 | 0.67 | 0.484144 |
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Target: 5'- -cUCCGAuuguguuGCCuCAUUAcuugcGGCCaUCUCCa -3' miRNA: 3'- auAGGUUu------CGGuGUAAU-----UCGG-AGAGG- -5' |
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| 12309 | 3' | -48.1 | NC_003323.1 | + | 3685 | 0.66 | 0.522411 |
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Target: 5'- --gUCGGGGCCAUGgagGAGCCUUUUg -3' miRNA: 3'- auaGGUUUCGGUGUaa-UUCGGAGAGg -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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