miRNA: 3'- -UGGaGAa-----CUCU--UUC--AUUCUCCCCUUU- -5'
miRNA: 3'- -UGGAGAACU-------------CuuUCauUCUCCCCUUU- -5'
miRNA: 3'- uGGAGaaCUCUUUCa-UUCuCCCCUUU- -5'
miRNA: 3'- -UGGAGAaCUCuuu--CAUUCUCC-CCUUU- -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 | |||||||
| 28554 | 3' | -48.6 | NC_005946.1 | + | 97931 | 0.67 | 0.98768 |
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Target: 5'- gGCCgCUgucucgGAGAagAAGaaUGGGAGGGGAAGa -3' miRNA: 3'- -UGGaGAa-----CUCU--UUC--AUUCUCCCCUUU- -5' |
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| 28554 | 3' | -48.6 | NC_005946.1 | + | 57915 | 0.67 | 0.987514 |
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Target: 5'- cACCUCUUGGcugccagggcccuGuuGGccGGGGGGGAGAg -3' miRNA: 3'- -UGGAGAACU-------------CuuUCauUCUCCCCUUU- -5' |
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| 28554 | 3' | -48.6 | NC_005946.1 | + | 12706 | 0.69 | 0.960755 |
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Target: 5'- uCCUCg-GAGGAGGggAGGuGGGGAGAc -3' miRNA: 3'- uGGAGaaCUCUUUCa-UUCuCCCCUUU- -5' |
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| 28554 | 3' | -48.6 | NC_005946.1 | + | 58218 | 0.73 | 0.827298 |
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Target: 5'- cACCUCUgGAGuguuuGUGAGGGGaGGAGAg -3' miRNA: 3'- -UGGAGAaCUCuuu--CAUUCUCC-CCUUU- -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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