miRNA: 3'- uGCGACU---ACGuCCggCACUACCUaua -5'
miRNA: 3'- -UGCGACUACGUCCGGCACUACCUAUA- -5'
miRNA: 3'- -UGCGACuaCGUCCGGCACUaccuaua -5'
miRNA: 3'- -UGCGACuaCGUCCGG---------CACUA------------CCUAUa -5'
miRNA: 3'- -UGcGACuaCGUC-----CGGCACUACCUaua -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 | |||||||
| 1078 | 5' | -54.4 | NC_000929.1 | + | 27256 | 0.69 | 0.411757 |
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Target: 5'- cCGCUGGcugUGCcGGuuGUGGUGGAc-- -3' miRNA: 3'- uGCGACU---ACGuCCggCACUACCUaua -5' |
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| 1078 | 5' | -54.4 | NC_000929.1 | + | 15285 | 1.05 | 0.001114 |
|
Target: 5'- cACGCUGAUGCAGGCCGUGAUGGAUAUc -3' miRNA: 3'- -UGCGACUACGUCCGGCACUACCUAUA- -5' |
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| 1078 | 5' | -54.4 | NC_000929.1 | + | 3023 | 0.74 | 0.202243 |
|
Target: 5'- gAUGCUGcgGCAGGCCGUGAa------ -3' miRNA: 3'- -UGCGACuaCGUCCGGCACUaccuaua -5' |
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| 1078 | 5' | -54.4 | NC_000929.1 | + | 30971 | 0.69 | 0.401961 |
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Target: 5'- uGCGCUGgcGCAGGCCaucagcgacGUGAUugccacugcggcGGAUGa -3' miRNA: 3'- -UGCGACuaCGUCCGG---------CACUA------------CCUAUa -5' |
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| 1078 | 5' | -54.4 | NC_000929.1 | + | 26719 | 0.68 | 0.462861 |
|
Target: 5'- gGCaCUGcgGCGGcaaccGCCGUGAUGGAa-- -3' miRNA: 3'- -UGcGACuaCGUC-----CGGCACUACCUaua -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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