miRNA: 3'- -CAUCUGC-----CGGC-UCAGGG-CGGUAGCuc -5'
miRNA: 3'- cauCUGCCGgcUCaGGGCGGUAGCUc -5'
miRNA: 3'- -CAUCUGCCGGCuc--AGG---GCGGuAGCUc -5'
miRNA: 3'- caUCUGCCGG------CUCAG------------GGCGGUAGCuc -5'
miRNA: 3'- -CAUCUGCCGGCUCAGGGCGGUAGCUC- -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 | |||||||
| 11418 | 3' | -58.3 | NC_003085.1 | + | 32355 | 0.67 | 0.444182 |
|
Target: 5'- gGUAGGCGuccuuGCCGuGGUCCCuGCCGUUGu- -3' miRNA: 3'- -CAUCUGC-----CGGC-UCAGGG-CGGUAGCuc -5' |
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| 11418 | 3' | -58.3 | NC_003085.1 | + | 24086 | 0.67 | 0.463632 |
|
Target: 5'- --cGACGGUgaAG-CCCGCCGUCGGc -3' miRNA: 3'- cauCUGCCGgcUCaGGGCGGUAGCUc -5' |
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| 11418 | 3' | -58.3 | NC_003085.1 | + | 32396 | 0.66 | 0.514088 |
|
Target: 5'- uGUGGGCGGCCGuacuUCUcgaCGCCcUCGAa -3' miRNA: 3'- -CAUCUGCCGGCuc--AGG---GCGGuAGCUc -5' |
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| 11418 | 3' | -58.3 | NC_003085.1 | + | 21934 | 0.66 | 0.534898 |
|
Target: 5'- -gAGAUGGCCacgaggGAGUCaucaugccggcgCCGCCGUCGu- -3' miRNA: 3'- caUCUGCCGG------CUCAG------------GGCGGUAGCuc -5' |
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| 11418 | 3' | -58.3 | NC_003085.1 | + | 43756 | 1.09 | 0.000473 |
|
Target: 5'- aGUAGACGGCCGAGUCCCGCCAUCGAGg -3' miRNA: 3'- -CAUCUGCCGGCUCAGGGCGGUAGCUC- -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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