miRNA: 3'- uGGGUUCuGUGGuuCCGCCcGUUCUC- -5'
miRNA: 3'- uGGGuUCUGUGGUUCCGCc--CG---UUCUC- -5'
miRNA: 3'- uGGGUU----CUG--UGGuUCCGCCCGU---UCUC- -5'
miRNA: 3'- -UGGGUUCUGUGGUUCCGCCCGUUCUC- -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 | |||||||
| 1317 | 5' | -56.2 | NC_001331.1 | + | 7019 | 0.66 | 0.15841 |
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Target: 5'- uCCCGAG-CACUc-GGCGG-CAAGAGc -3' miRNA: 3'- uGGGUUCuGUGGuuCCGCCcGUUCUC- -5' |
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| 1317 | 5' | -56.2 | NC_001331.1 | + | 415 | 0.67 | 0.130457 |
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Target: 5'- uCUCcGGACGCCAAGGCGuaaGCcuuAGGAGg -3' miRNA: 3'- uGGGuUCUGUGGUUCCGCc--CG---UUCUC- -5' |
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| 1317 | 5' | -56.2 | NC_001331.1 | + | 1963 | 0.67 | 0.110717 |
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Target: 5'- cCCCGAccacGACcaGCC-GGGCGGGCAgccGGGGu -3' miRNA: 3'- uGGGUU----CUG--UGGuUCCGCCCGU---UCUC- -5' |
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| 1317 | 5' | -56.2 | NC_001331.1 | + | 3535 | 1.08 | 4.5e-05 |
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Target: 5'- gACCCAAGACACCAAGGCGGGCAAGAGc -3' miRNA: 3'- -UGGGUUCUGUGGUUCCGCCCGUUCUC- -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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