miRNA: 3'- -CAGUAGGCCUGCUGCCGUCAGUCGCU- -5'
miRNA: 3'- caguaGGCCUGCUGCCGUCaGUCGCU- -5'
miRNA: 3'- -CAGu---AGGCC-UGC---UGCCGUcAGUCGCU- -5'
miRNA: 3'- -CAGUAGGCCUGCUGcCGUCaGUcg-CU- -5'
miRNA: 3'- cagUAGGCCUGCUG--------------CCGUCA--------GUCGCU- -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 |
| Predicted miRNA align pattern | |||||||
| 12752 | 3' | -56.8 | NC_003356.1 | + | 34433 | 1.09 | 0.000547 |
|
Target: 5'- aGUCAUCCGGACGACGGCAGUCAGCGAg -3' miRNA: 3'- -CAGUAGGCCUGCUGCCGUCAGUCGCU- -5' |
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| 12752 | 3' | -56.8 | NC_003356.1 | + | 41409 | 0.78 | 0.100286 |
|
Target: 5'- ----aCCGGACGAUGGCAG-CAGUGAg -3' miRNA: 3'- caguaGGCCUGCUGCCGUCaGUCGCU- -5' |
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| 12752 | 3' | -56.8 | NC_003356.1 | + | 19150 | 0.67 | 0.473859 |
|
Target: 5'- uGUCcgguUCCGGcACGgcuGCGGCGcUCGGCGGg -3' miRNA: 3'- -CAGu---AGGCC-UGC---UGCCGUcAGUCGCU- -5' |
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| 12752 | 3' | -56.8 | NC_003356.1 | + | 34490 | 0.7 | 0.319645 |
|
Target: 5'- cGUCGUCCGGAUGACuGCAGcCAccaGAu -3' miRNA: 3'- -CAGUAGGCCUGCUGcCGUCaGUcg-CU- -5' |
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| 12752 | 3' | -56.8 | NC_003356.1 | + | 34075 | 0.69 | 0.366921 |
|
Target: 5'- --aAUCCGGACGACuccuccaguuuucuGGCGGUugcggcucCGGCGAc -3' miRNA: 3'- cagUAGGCCUGCUG--------------CCGUCA--------GUCGCU- -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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