miRNA: 3'- gCCUuuGGG--CUCG-----UAACA------------ACUCCGAC- -5'
miRNA: 3'- -GCCUUUGGGC----UCGUaaCAa--CUCCGac -5'
miRNA: 3'- gCCUUUG-GGCuCGUaaca-ACUCCGAc -5'
miRNA: 3'- gCCU---UUGggCUCGUAa-CAACUCCGac -5'
miRNA: 3'- -GCCUUUGGGCUCGUAACAACUCCGAC- -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 | |||||||
| 18237 | 5' | -51.9 | NC_004680.1 | + | 39461 | 0.66 | 0.890786 |
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Target: 5'- uGGAuuCCCcaGAGUgggggGUUGUccgguuugcggaUGAGGCUGg -3' miRNA: 3'- gCCUuuGGG--CUCG-----UAACA------------ACUCCGAC- -5' |
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| 18237 | 5' | -51.9 | NC_004680.1 | + | 8798 | 0.66 | 0.86736 |
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Target: 5'- gCGGAGACCCGucccGGCGcgGUcaaGGGGCc- -3' miRNA: 3'- -GCCUUUGGGC----UCGUaaCAa--CUCCGac -5' |
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| 18237 | 5' | -51.9 | NC_004680.1 | + | 47786 | 0.67 | 0.850451 |
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Target: 5'- gGGAGACuCCG-GCGgaacgUGAGGCUc -3' miRNA: 3'- gCCUUUG-GGCuCGUaaca-ACUCCGAc -5' |
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| 18237 | 5' | -51.9 | NC_004680.1 | + | 9390 | 0.68 | 0.763663 |
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Target: 5'- uGGAgaaAGCgaGAGCGUcgGUUGAGGCg- -3' miRNA: 3'- gCCU---UUGggCUCGUAa-CAACUCCGac -5' |
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| 18237 | 5' | -51.9 | NC_004680.1 | + | 54752 | 1.09 | 0.002397 |
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Target: 5'- aCGGAAACCCGAGCAUUGUUGAGGCUGc -3' miRNA: 3'- -GCCUUUGGGCUCGUAACAACUCCGAC- -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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