miRNA: 3'- uaCACCGGCAAGauaGGUCCaCGUag -5'
miRNA: 3'- uaCACCGGCAaga-UAGGUCCaCGUAG- -5'
miRNA: 3'- -UACaCCGgCAAGAUa----GGUCCACGUAG- -5'
miRNA: 3'- -UACACCGGCAAGAUAGGUCCACGUAG- -5'
Results 1 - 4 of 4 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 | |||||||
| 28399 | 5' | -53.6 | NC_005946.1 | + | 13147 | 0.66 | 0.905287 |
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Target: 5'- -gGUGGCUGUUC---CCAGGgGCAg- -3' miRNA: 3'- uaCACCGGCAAGauaGGUCCaCGUag -5' |
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| 28399 | 5' | -53.6 | NC_005946.1 | + | 73806 | 0.68 | 0.799207 |
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Target: 5'- -gGUGGCUGUgcgaGUUCAGGaGCGUCa -3' miRNA: 3'- uaCACCGGCAaga-UAGGUCCaCGUAG- -5' |
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| 28399 | 5' | -53.6 | NC_005946.1 | + | 84113 | 0.72 | 0.567583 |
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Target: 5'- gGUGgGGUgGUUCUGccacgUCAGGUGCGUCa -3' miRNA: 3'- -UACaCCGgCAAGAUa----GGUCCACGUAG- -5' |
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| 28399 | 5' | -53.6 | NC_005946.1 | + | 60982 | 1.09 | 0.002641 |
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Target: 5'- gAUGUGGCCGUUCUAUCCAGGUGCAUCa -3' miRNA: 3'- -UACACCGGCAAGAUAGGUCCACGUAG- -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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