miRNA: 3'- -AUUUGCGGGCGGCUGu----UUGGUccuga -5'
miRNA: 3'- aUUUGCGGGCG-GCUGuUUggUCCUGa -5'
miRNA: 3'- -AUUUGc-GGGCGGCU-GUU-----UGGUCCUGA- -5'
miRNA: 3'- -AUUUGCGGGCGGCUGUUUGGUCCUGA- -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 | |||||||
| 8449 | 5' | -54.4 | NC_002167.1 | + | 208 | 0.67 | 0.593053 |
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Target: 5'- cUGGACGCCUGCCGACcuucuAGCCGc---- -3' miRNA: 3'- -AUUUGCGGGCGGCUGu----UUGGUccuga -5' |
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| 8449 | 5' | -54.4 | NC_002167.1 | + | 10932 | 0.67 | 0.570381 |
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Target: 5'- aGAGCGCCUGCgCGACcAGgaGGGAUa -3' miRNA: 3'- aUUUGCGGGCG-GCUGuUUggUCCUGa -5' |
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| 8449 | 5' | -54.4 | NC_002167.1 | + | 1750 | 0.69 | 0.45124 |
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Target: 5'- cUGAGCcuCCCGCUGGuCGAguucgGCCAGGGCUu -3' miRNA: 3'- -AUUUGc-GGGCGGCU-GUU-----UGGUCCUGA- -5' |
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| 8449 | 5' | -54.4 | NC_002167.1 | + | 2180 | 1.05 | 0.00131 |
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Target: 5'- cUAAACGCCCGCCGACAAACCAGGACUu -3' miRNA: 3'- -AUUUGCGGGCGGCUGUUUGGUCCUGA- -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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