miRNA: 3'- uGUGuCCGUAUACUGaa----UACAAA-UGU- -5'
miRNA: 3'- -UGugU-CC-GUAUACUGAauaCAAAUGU- -5'
miRNA: 3'- -UGUGuCCGUA--UACUGaa-----------UACAAAUGU- -5'
miRNA: 3'- uGUGUCCgUAUAcUGAAUACAAAUGU- -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 | |||||||
| 28571 | 5' | -43 | NC_005946.1 | + | 96822 | 0.66 | 0.999996 |
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Target: 5'- uCGC-GGCGUAUGGCgugcugAUGUUUcACAc -3' miRNA: 3'- uGUGuCCGUAUACUGaa----UACAAA-UGU- -5' |
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| 28571 | 5' | -43 | NC_005946.1 | + | 91754 | 0.67 | 0.999992 |
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Target: 5'- uGCugGuGGaCAUGUGGCUggcGUUUGCGa -3' miRNA: 3'- -UGugU-CC-GUAUACUGAauaCAAAUGU- -5' |
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| 28571 | 5' | -43 | NC_005946.1 | + | 59426 | 0.69 | 0.999827 |
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Target: 5'- gACGCuGGCGUccAUGGCgcacgaacugaggAUGUUUGCAa -3' miRNA: 3'- -UGUGuCCGUA--UACUGaa-----------UACAAAUGU- -5' |
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| 28571 | 5' | -43 | NC_005946.1 | + | 105123 | 0.82 | 0.775115 |
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Target: 5'- uCACAGGgGUGUuACUUAUGUUUACAc -3' miRNA: 3'- uGUGUCCgUAUAcUGAAUACAAAUGU- -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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