miRNA: 3'- -GGgAGGAGGUUGCG-GUCUGCUc---CUUU- -5'
miRNA: 3'- ggGAGGAGGUU---------------GCGGUCugCuCCUUU- -5'
miRNA: 3'- -GGGAGgAGGUUGCGGUCUgCUCCuuU- -5'
miRNA: 3'- -GGGAg-------GAGg--UUGCGGUCUgCUCCUUu -5'
miRNA: 3'- -GGGAGGAGGUUGCGGUCUGCUCCUUU- -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 | |||||||
| 30301 | 3' | -56 | NC_006324.1 | + | 9359 | 0.67 | 0.44346 |
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Target: 5'- aCCgUCUUCCGAUGCgCAGACGGcgccGAAGa -3' miRNA: 3'- -GGgAGGAGGUUGCG-GUCUGCUc---CUUU- -5' |
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| 30301 | 3' | -56 | NC_006324.1 | + | 16037 | 0.68 | 0.437436 |
|
Target: 5'- -gCUCCUCCAGaaauaaagccaccagUGUCAGugGuGGAGAa -3' miRNA: 3'- ggGAGGAGGUU---------------GCGGUCugCuCCUUU- -5' |
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| 30301 | 3' | -56 | NC_006324.1 | + | 24319 | 0.71 | 0.285369 |
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Target: 5'- uUCCUCgUCUGGCGUUGGAgGAGGggGu -3' miRNA: 3'- -GGGAGgAGGUUGCGGUCUgCUCCuuU- -5' |
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| 30301 | 3' | -56 | NC_006324.1 | + | 12381 | 0.71 | 0.26379 |
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Target: 5'- uCCCUaaagaguaCUCauuGACGCCAGAgGAGGAGc -3' miRNA: 3'- -GGGAg-------GAGg--UUGCGGUCUgCUCCUUu -5' |
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| 30301 | 3' | -56 | NC_006324.1 | + | 24261 | 1.08 | 0.00056 |
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Target: 5'- cCCCUCCUCCAACGCCAGACGAGGAAAc -3' miRNA: 3'- -GGGAGGAGGUUGCGGUCUGCUCCUUU- -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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