miRNA: 3'- -UGC-UCUU---UGUCC-CGCUg-GCCGCaCGC- -5'
miRNA: 3'- uGCUCUu-UGU-----CCCGCUGG-----CCGCACGc -5'
miRNA: 3'- -UGCU-CUUUGUcCCGCuGGCCGC----------ACGC- -5'
miRNA: 3'- uGCUC--UUUGUC-CC---GCUgGCCGCACGC- -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 |
| Predicted miRNA align pattern | |||||||
| 12232 | 3' | -57.8 | NC_003309.1 | + | 13644 | 0.66 | 0.591459 |
|
Target: 5'- gACGaAGAGuccGCGGGcGCGAagCGGCG-GCGu -3' miRNA: 3'- -UGC-UCUU---UGUCC-CGCUg-GCCGCaCGC- -5' |
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| 12232 | 3' | -57.8 | NC_003309.1 | + | 32878 | 0.66 | 0.570056 |
|
Target: 5'- uCGGGAcuGCAaauguGGGCGAUCcagaaGGCGUGCu -3' miRNA: 3'- uGCUCUu-UGU-----CCCGCUGG-----CCGCACGc -5' |
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| 12232 | 3' | -57.8 | NC_003309.1 | + | 7776 | 0.66 | 0.548848 |
|
Target: 5'- cACGAcGAAAUAcGGCG-CCGGCGccuucgccggUGCGa -3' miRNA: 3'- -UGCU-CUUUGUcCCGCuGGCCGC----------ACGC- -5' |
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| 12232 | 3' | -57.8 | NC_003309.1 | + | 29607 | 0.7 | 0.349223 |
|
Target: 5'- cCGAGcaAAACGGuGGauuCGAgCGGCGUGCGg -3' miRNA: 3'- uGCUC--UUUGUC-CC---GCUgGCCGCACGC- -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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