miRNA: 3'- gAGUGUGCG-------------UGCGAcAUGCaGCGGCu -5'
miRNA: 3'- gaGUGUGCGuGCGaca-UGCAG---CGGCU- -5'
miRNA: 3'- gaGUG--UGCGu--GCGa-CAUGCaGCGGCU- -5'
Results 21 - 23 of 23 are showing below:
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| ID | Location | Perfect MFE.* | RefSeq Acc. | strand | Start Position | R_P_ratio# |
P value
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| Predicted miRNA align pattern | |||||||
| 12113 | 3' | -55.5 | NC_003309.1 | + | 10599 | 0.66 | 0.725573 |
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Target: 5'- uUCGCGCGUgccgucgcgacauGCGCU-UGCGcCGCCGc -3' miRNA: 3'- gAGUGUGCG-------------UGCGAcAUGCaGCGGCu -5' |
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| 12113 | 3' | -55.5 | NC_003309.1 | + | 11969 | 0.66 | 0.72663 |
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Target: 5'- -gCGCGCGC-CGCgucgGCGUUgaaGCCGAa -3' miRNA: 3'- gaGUGUGCGuGCGaca-UGCAG---CGGCU- -5' |
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| 12113 | 3' | -55.5 | NC_003309.1 | + | 7762 | 0.66 | 0.72663 |
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Target: 5'- -gCGCcgGCGCcuuCGCcgGUGCGaCGCCGAg -3' miRNA: 3'- gaGUG--UGCGu--GCGa-CAUGCaGCGGCU- -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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