miRNA: 3'- caACGCGCUuu--GCGUGaCGACGaacu -5'
miRNA: 3'- -CAAC-GCGCUUUGCGUGa---CGACg-------AACU- -5'
miRNA: 3'- caaCGCGCuuu-GCGuGACGA------CGAACU- -5'
miRNA: 3'- caACGCGCUu-UG-CGUGACGaCGAacu -5'
miRNA: 3'- -CAACGCGCUUUGCGUGACGACGAACU- -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
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| Predicted miRNA align pattern | |||||||
| 12143 | 3' | -51.7 | NC_003309.1 | + | 22457 | 0.66 | 0.856042 |
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Target: 5'- -gUGCGCGGcgauCGCAC-GCUGCc--- -3' miRNA: 3'- caACGCGCUuu--GCGUGaCGACGaacu -5' |
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| 12143 | 3' | -51.7 | NC_003309.1 | + | 14334 | 0.66 | 0.847199 |
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Target: 5'- cGUUGaCGCGAAACGUAUggucGCUGaguagguaUUGGu -3' miRNA: 3'- -CAAC-GCGCUUUGCGUGa---CGACg-------AACU- -5' |
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| 12143 | 3' | -51.7 | NC_003309.1 | + | 3459 | 0.66 | 0.83811 |
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Target: 5'- --cGCGCGucuuCGC-CUGCUcaugccGCUUGAc -3' miRNA: 3'- caaCGCGCuuu-GCGuGACGA------CGAACU- -5' |
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| 12143 | 3' | -51.7 | NC_003309.1 | + | 48694 | 0.67 | 0.80947 |
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Target: 5'- -gUGCGCGAucGCuGCGCUGC-GCUc-- -3' miRNA: 3'- caACGCGCUu-UG-CGUGACGaCGAacu -5' |
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| 12143 | 3' | -51.7 | NC_003309.1 | + | 25660 | 1.09 | 0.001716 |
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Target: 5'- gGUUGCGCGAAACGCACUGCUGCUUGAg -3' miRNA: 3'- -CAACGCGCUUUGCGUGACGACGAACU- -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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