miRNA: 3'- guuCGugUuCCCC----AC-CGACGGGCU-CU- -5'
miRNA: 3'- guuCGUGuuCCCCA---------------CCgACGGGCUCU- -5'
miRNA: 3'- -GUUCGUGUUCC----CCA--CCGACGG-GCuCU- -5'
miRNA: 3'- -GUUCGUGuucCCCAC-CGACGGGC-UCu -5'
miRNA: 3'- -GUUCGUGUUCCCCACCGACGGGCUCU- -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 | |||||||
| 23268 | 5' | -58.2 | NC_005259.1 | + | 37621 | 0.66 | 0.607731 |
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Target: 5'- --cGCugAuGGGGaugaUGuGCUGCCCGAuGAc -3' miRNA: 3'- guuCGugUuCCCC----AC-CGACGGGCU-CU- -5' |
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| 23268 | 5' | -58.2 | NC_005259.1 | + | 31932 | 0.67 | 0.548195 |
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Target: 5'- --cGCACucGGGGUcgaggcgguuaccucGGgUGCCUGAGGu -3' miRNA: 3'- guuCGUGuuCCCCA---------------CCgACGGGCUCU- -5' |
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| 23268 | 5' | -58.2 | NC_005259.1 | + | 8646 | 0.69 | 0.406399 |
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Target: 5'- gCGGGCACGAGGcuguGGUcgGGCUGCCaCGcGGg -3' miRNA: 3'- -GUUCGUGUUCC----CCA--CCGACGG-GCuCU- -5' |
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| 23268 | 5' | -58.2 | NC_005259.1 | + | 20524 | 0.7 | 0.346258 |
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Target: 5'- cCGAGCAC---GGGUGcGCUGCCCGcAGc -3' miRNA: 3'- -GUUCGUGuucCCCAC-CGACGGGC-UCu -5' |
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| 23268 | 5' | -58.2 | NC_005259.1 | + | 29899 | 1.08 | 0.000726 |
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Target: 5'- gCAAGCACAAGGGGUGGCUGCCCGAGAc -3' miRNA: 3'- -GUUCGUGUUCCCCACCGACGGGCUCU- -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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