miRNA: 3'- uCGC-CAAGCgGCACUA-GCUGCu----CCUG- -5'
miRNA: 3'- uCGCCAAGCGgcACUAGCUGCUcCUG- -5'
miRNA: 3'- uCGCCaaGCGgcACUAGCUGCU-CCUg -5'
miRNA: 3'- -UCGCCA----AGCGGC---------ACUAGCUGCu--CCUG- -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 | |||||||
| 12229 | 5' | -56.3 | NC_003309.1 | + | 17794 | 0.66 | 0.633531 |
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Target: 5'- uGCGcGUUCGgCGUGAUaCGGCGcacacGGAUc -3' miRNA: 3'- uCGC-CAAGCgGCACUA-GCUGCu----CCUG- -5' |
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| 12229 | 5' | -56.3 | NC_003309.1 | + | 22502 | 0.68 | 0.568471 |
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Target: 5'- cGUGGUUCGU--UGGUCGACGGcGGCc -3' miRNA: 3'- uCGCCAAGCGgcACUAGCUGCUcCUG- -5' |
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| 12229 | 5' | -56.3 | NC_003309.1 | + | 25761 | 0.69 | 0.474701 |
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Target: 5'- cGCGGagCGCa-UGAUCGGCGAcGGAg -3' miRNA: 3'- uCGCCaaGCGgcACUAGCUGCU-CCUg -5' |
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| 12229 | 5' | -56.3 | NC_003309.1 | + | 5546 | 0.74 | 0.232631 |
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Target: 5'- cGGCGGUgaggUCGCCGaccacgaucUGAUCGACGuucGGAUu -3' miRNA: 3'- -UCGCCA----AGCGGC---------ACUAGCUGCu--CCUG- -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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