miRNA: 3'- gCGUCguaUUCCA--GUUG------CUCCCGAGC- -5'
miRNA: 3'- gCGUCG--UAUUCCAgUUGCU----CCCG--AGC- -5'
miRNA: 3'- gCGUCGUAuuCC-AGU-----UGCUCCCGaGC- -5'
miRNA: 3'- gCGUC-GUAU-UCCAGUUGCUccCGAGC- -5'
miRNA: 3'- -GCGUCGUAUUCCAGUUGCUCCCGAGC- -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 | |||||||
| 10692 | 3' | -53.6 | NC_002786.1 | + | 6177 | 0.66 | 0.197182 |
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Target: 5'- gGCAGag-GGGGUggCAGCcccagaGGGGGCUCGc -3' miRNA: 3'- gCGUCguaUUCCA--GUUG------CUCCCGAGC- -5' |
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| 10692 | 3' | -53.6 | NC_002786.1 | + | 471 | 0.66 | 0.184901 |
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Target: 5'- gGUAGUugAUGAGGUgGGCGAaguuGGGCugUCGg -3' miRNA: 3'- gCGUCG--UAUUCCAgUUGCU----CCCG--AGC- -5' |
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| 10692 | 3' | -53.6 | NC_002786.1 | + | 2116 | 0.67 | 0.167747 |
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Target: 5'- gGCGGUGUcuGGcUCAggagcGCGAGGGC-CGg -3' miRNA: 3'- gCGUCGUAuuCC-AGU-----UGCUCCCGaGC- -5' |
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| 10692 | 3' | -53.6 | NC_002786.1 | + | 4742 | 0.68 | 0.142311 |
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Target: 5'- gGUAGaCGUGcAGGUCGACGA--GCUCGg -3' miRNA: 3'- gCGUC-GUAU-UCCAGUUGCUccCGAGC- -5' |
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| 10692 | 3' | -53.6 | NC_002786.1 | + | 4398 | 1.09 | 0.000058 |
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Target: 5'- aCGCAGCAUAAGGUCAACGAGGGCUCGc -3' miRNA: 3'- -GCGUCGUAUUCCAGUUGCUCCCGAGC- -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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