miRNA: 3'- aCAGGUUC--CGGUAg---------GCUCAGCGUaua -5'
miRNA: 3'- aCAGGUU---CCGGUAGGcUCAGcGUaua -5'
miRNA: 3'- aCAG-----GUUCCGGUaGGCUCAGCGUaua -5'
miRNA: 3'- -ACAGGUUCCGGUAGGCUCAGCGUAUA- -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 | |||||||
| 1450 | 5' | -54 | NC_001335.1 | + | 2003 | 0.66 | 0.741712 |
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Target: 5'- cGUCCAGGguGCCGUacuucuugaaCGAGUCGUAc-- -3' miRNA: 3'- aCAGGUUC--CGGUAg---------GCUCAGCGUaua -5' |
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| 1450 | 5' | -54 | NC_001335.1 | + | 49572 | 0.66 | 0.720001 |
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Target: 5'- cGUCCAGcgcGGCCAUCCaGGUCuCGa-- -3' miRNA: 3'- aCAGGUU---CCGGUAGGcUCAGcGUaua -5' |
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| 1450 | 5' | -54 | NC_001335.1 | + | 25358 | 0.67 | 0.641754 |
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Target: 5'- cGUCgugaaCAAGGCUA-CCGGGUUGCAa-- -3' miRNA: 3'- aCAG-----GUUCCGGUaGGCUCAGCGUaua -5' |
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| 1450 | 5' | -54 | NC_001335.1 | + | 8876 | 1.07 | 0.001564 |
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Target: 5'- gUGUCCAAGGCCAUCCGAGUCGCAUAUg -3' miRNA: 3'- -ACAGGUUCCGGUAGGCUCAGCGUAUA- -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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