miRNA: 3'- uCGAGCGGUU---CGAGU--------UGCCG-CAC---UUG- -5'
miRNA: 3'- -UCG--AGCGGUUCGaGUUGcCGC-------ACUUG- -5'
miRNA: 3'- -UCGAGCGGUUcgaGUUGCCGCaCUUG- -5'
miRNA: 3'- -UCGAgCGGUUCgAGuuGCCgCA-CUUG- -5'
Results 21 - 24 of 24 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 | |||||||
| 11952 | 3' | -54.7 | NC_003278.1 | + | 5082 | 0.71 | 0.319102 |
|
Target: 5'- uGCUCGCCGAguuGCUCAcccaggucGCGGCuGUGcucGGCg -3' miRNA: 3'- uCGAGCGGUU---CGAGU--------UGCCG-CAC---UUG- -5' |
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| 11952 | 3' | -54.7 | NC_003278.1 | + | 4999 | 0.67 | 0.534196 |
|
Target: 5'- aAGCgaUCGCCGAGCaCAGCcGCGaccugggUGAGCa -3' miRNA: 3'- -UCG--AGCGGUUCGaGUUGcCGC-------ACUUG- -5' |
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| 11952 | 3' | -54.7 | NC_003278.1 | + | 3163 | 0.67 | 0.513143 |
|
Target: 5'- cAGUUCGUCGA---CGACGGCGcGAGCa -3' miRNA: 3'- -UCGAGCGGUUcgaGUUGCCGCaCUUG- -5' |
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| 11952 | 3' | -54.7 | NC_003278.1 | + | 2298 | 0.69 | 0.39934 |
|
Target: 5'- gGGCUgGCCAAG-UCggUGGgGUcGAGCg -3' miRNA: 3'- -UCGAgCGGUUCgAGuuGCCgCA-CUUG- -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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