miRNA: 3'- -GCGcGCUAGua-AGUAGGcUGGCUGCU- -5'
miRNA: 3'- gcgCGCUAGUAa--GUAGGCuG-GCUGCu -5'
miRNA: 3'- gCGCGCU-----AGUAAGUa----GGCUGGCUGcu -5'
miRNA: 3'- -GCGCGCUAGuaaGUaGGCUG-GCUGcu -5'
miRNA: 3'- gcGCGCUAGUAAGU---------AGGCUGGCUGCu -5'
Results 21 - 25 of 25 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 | |||||||
| 27927 | 5' | -53 | NC_005886.2 | + | 38769 | 0.72 | 0.495749 |
|
Target: 5'- cCGCaCGAUCcgcUCAUCC-ACCGGCGAg -3' miRNA: 3'- -GCGcGCUAGua-AGUAGGcUGGCUGCU- -5' |
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| 27927 | 5' | -53 | NC_005886.2 | + | 38864 | 0.67 | 0.777975 |
|
Target: 5'- --aGCGAUCAUggcCGUCCGuCgCGACGu -3' miRNA: 3'- gcgCGCUAGUAa--GUAGGCuG-GCUGCu -5' |
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| 27927 | 5' | -53 | NC_005886.2 | + | 42036 | 0.74 | 0.378749 |
|
Target: 5'- gGCGCGAacacuUCGUUCAgcgugUCGGCCGGCa- -3' miRNA: 3'- gCGCGCU-----AGUAAGUa----GGCUGGCUGcu -5' |
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| 27927 | 5' | -53 | NC_005886.2 | + | 45927 | 0.66 | 0.844394 |
|
Target: 5'- gCGCGCGAUCug-CG-CCGAUgCGGCu- -3' miRNA: 3'- -GCGCGCUAGuaaGUaGGCUG-GCUGcu -5' |
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| 27927 | 5' | -53 | NC_005886.2 | + | 46956 | 0.74 | 0.378749 |
|
Target: 5'- -aUGCGAUCAUUCGcauugccgaUCUGGCCGGCGc -3' miRNA: 3'- gcGCGCUAGUAAGU---------AGGCUGGCUGCu -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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