miRNA: 3'- -AAC-GCCGa--CCUUGUAG----UGGGGUuUUC- -5'
miRNA: 3'- aaCGCCGACCUUGUaGU------GGGGUuuuc -5'
miRNA: 3'- aACGCCGACc----UUGUAGUG-GGGUuUUC- -5'
miRNA: 3'- -AACGCCGACCUUGUAGUGGGGUUUUC- -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 | |||||||
| 31987 | 3' | -52.5 | NC_006948.1 | + | 1437 | 0.66 | 0.189916 |
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Target: 5'- gUUGuCGGCgcgGGGGCGUCggggGCCUCAcAGGg -3' miRNA: 3'- -AAC-GCCGa--CCUUGUAG----UGGGGUuUUC- -5' |
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| 31987 | 3' | -52.5 | NC_006948.1 | + | 5319 | 0.69 | 0.11801 |
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Target: 5'- -cGCGGCUGGAACGcCAaggcguUCCCAc--- -3' miRNA: 3'- aaCGCCGACCUUGUaGU------GGGGUuuuc -5' |
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| 31987 | 3' | -52.5 | NC_006948.1 | + | 1761 | 0.72 | 0.072136 |
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Target: 5'- aUGCGGCUGuucuuGACGUCGCuCCCGuAAGc -3' miRNA: 3'- aACGCCGACc----UUGUAGUG-GGGUuUUC- -5' |
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| 31987 | 3' | -52.5 | NC_006948.1 | + | 3755 | 1.08 | 0.00007 |
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Target: 5'- uUUGCGGCUGGAACAUCACCCCAAAAGg -3' miRNA: 3'- -AACGCCGACCUUGUAGUGGGGUUUUC- -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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