miRNA: 3'- -CCCUACGGCCGGUaa---GGUACUuCaCG- -5'
miRNA: 3'- -CCC------UACggCCGGuaAGGUACUu--CACG- -5'
miRNA: 3'- -CCCUACGGCCG-GUAAGGUACU-----UCA-CG- -5'
miRNA: 3'- -CCCUACGGCCGGUAAGGUACUUCACG- -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 | |||||||
| 2850 | 3' | -53 | NC_001492.1 | + | 9165 | 0.72 | 0.170957 |
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Target: 5'- cGGGGUGCCGGUCAcgcacUCGUGAcG-GCa -3' miRNA: 3'- -CCCUACGGCCGGUaa---GGUACUuCaCG- -5' |
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| 2850 | 3' | -53 | NC_001492.1 | + | 2447 | 0.73 | 0.133195 |
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Target: 5'- aGGGcaguccAUGuuGGCCcgUCCAUGAccuGUGUu -3' miRNA: 3'- -CCC------UACggCCGGuaAGGUACUu--CACG- -5' |
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| 2850 | 3' | -53 | NC_001492.1 | + | 2794 | 0.78 | 0.053813 |
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Target: 5'- uGGGAUGUCGGCgUGUUCCGUGAccgcaGGUcGCu -3' miRNA: 3'- -CCCUACGGCCG-GUAAGGUACU-----UCA-CG- -5' |
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| 2850 | 3' | -53 | NC_001492.1 | + | 10729 | 1.15 | 7.2e-05 |
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Target: 5'- aGGGAUGCCGGCCAUUCCAUGAAGUGCa -3' miRNA: 3'- -CCCUACGGCCGGUAAGGUACUUCACG- -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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