miRNA: 3'- -GCaaaCAGGGGG---GG-------------AGCUAGCUCGAG- -5'
miRNA: 3'- gcaaaCAG-GGGGGGaGCUAGCUCGAg -5'
miRNA: 3'- -GCAAaCaGGGGGG------GAGCUAGCuCGAG- -5'
miRNA: 3'- -GCAAACAGGGGGGGAGCUAGCUCGAG- -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 | |||||||
| 2905 | 3' | -56.4 | NC_001493.1 | + | 105343 | 0.66 | 0.874665 |
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Target: 5'- aCGgg-GUCUCCCgggUCgcgcagugugcgaUCGGUCGAGCUCa -3' miRNA: 3'- -GCaaaCAGGGGG---GG-------------AGCUAGCUCGAG- -5' |
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| 2905 | 3' | -56.4 | NC_001493.1 | + | 95638 | 0.66 | 0.868055 |
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Target: 5'- ----cGUCaCCUCCC-CGAUCGGGUUg -3' miRNA: 3'- gcaaaCAG-GGGGGGaGCUAGCUCGAg -5' |
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| 2905 | 3' | -56.4 | NC_001493.1 | + | 87381 | 0.69 | 0.736564 |
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Target: 5'- gCGUUgGaCCCCCCgagugaUUCGAUCG-GCUCg -3' miRNA: 3'- -GCAAaCaGGGGGG------GAGCUAGCuCGAG- -5' |
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| 2905 | 3' | -56.4 | NC_001493.1 | + | 31982 | 1.1 | 0.00203 |
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Target: 5'- gCGUUUGUCCCCCCCUCGAUCGAGCUCa -3' miRNA: 3'- -GCAAACAGGGGGGGAGCUAGCUCGAG- -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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