miRNA: 3'- cguaCGGUGU---UCCUGGG-----------AGGGUCugC- -5'
miRNA: 3'- -CGUAC-GGUGuUCCUGGGa---GG-GUCUGc -5'
miRNA: 3'- cGUACGGUgUUC-CUGGGAGGGuCUGC- -5'
miRNA: 3'- cGUA-CGGUGUUCC--------UgGGAGGGUCUGC- -5'
miRNA: 3'- -CGUACGGUGUUCCUGGGAGGGUCUGC- -5'
Results 1 - 5 of 5 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 | |||||||
| 29697 | 3' | -56.3 | NC_006269.1 | + | 3731 | 0.67 | 0.126335 |
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Target: 5'- ---gGCCACGcagGGGAUCUgugguaucgggUCCCAGugGg -3' miRNA: 3'- cguaCGGUGU---UCCUGGG-----------AGGGUCugC- -5' |
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| 29697 | 3' | -56.3 | NC_006269.1 | + | 3682 | 0.69 | 0.094159 |
|
Target: 5'- gGUAUGcCCACuGGGACCCgauaCCaCAGAUc -3' miRNA: 3'- -CGUAC-GGUGuUCCUGGGa---GG-GUCUGc -5' |
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| 29697 | 3' | -56.3 | NC_006269.1 | + | 239 | 0.7 | 0.074668 |
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Target: 5'- aCAUGUCA-AGGaGACCCUCCUcGACGa -3' miRNA: 3'- cGUACGGUgUUC-CUGGGAGGGuCUGC- -5' |
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| 29697 | 3' | -56.3 | NC_006269.1 | + | 2863 | 0.73 | 0.043609 |
|
Target: 5'- cCAUgGCCACAGGGccggagugAgCCUCUCAGACGa -3' miRNA: 3'- cGUA-CGGUGUUCC--------UgGGAGGGUCUGC- -5' |
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| 29697 | 3' | -56.3 | NC_006269.1 | + | 170 | 1.12 | 0.000023 |
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Target: 5'- aGCAUGCCACAAGGACCCUCCCAGACGg -3' miRNA: 3'- -CGUACGGUGUUCCUGGGAGGGUCUGC- -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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