miRNA: 3'- gCCCGGUaCAUGcGGCU------AUUACGAag -5'
miRNA: 3'- gCCCGGUa--CAUGc----GGCuauUACGAAG- -5'
miRNA: 3'- -GCCCggUACAug------CGGCUAUUACGAAG- -5'
miRNA: 3'- gCCCGgU---ACA--UGCGGCUAUUACGAAG- -5'
miRNA: 3'- -GCCCGGUACAUGCGGCUAUUACGAAG- -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 | |||||||
| 8676 | 5' | -51.8 | NC_002229.2 | + | 48408 | 0.66 | 0.988261 |
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Target: 5'- gGGGCCAcGUGCaCCGAgucugaUAGUGUUg- -3' miRNA: 3'- gCCCGGUaCAUGcGGCU------AUUACGAag -5' |
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| 8676 | 5' | -51.8 | NC_002229.2 | + | 28530 | 0.67 | 0.973751 |
|
Target: 5'- uGGGCCAgggGUGCacccuCCGc--AUGCUUCa -3' miRNA: 3'- gCCCGGUa--CAUGc----GGCuauUACGAAG- -5' |
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| 8676 | 5' | -51.8 | NC_002229.2 | + | 119240 | 0.68 | 0.957411 |
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Target: 5'- cCGGG--AUGUcugcaaaaGCCGAUGAUGCUUCc -3' miRNA: 3'- -GCCCggUACAug------CGGCUAUUACGAAG- -5' |
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| 8676 | 5' | -51.8 | NC_002229.2 | + | 21090 | 0.69 | 0.935204 |
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Target: 5'- aGGGUgGcauUGUccAUGCUGGUGAUGCUUUg -3' miRNA: 3'- gCCCGgU---ACA--UGCGGCUAUUACGAAG- -5' |
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| 8676 | 5' | -51.8 | NC_002229.2 | + | 67275 | 1.1 | 0.006623 |
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Target: 5'- gCGGGCCAUGUACGCCGAUAAUGCUUCu -3' miRNA: 3'- -GCCCGGUACAUGCGGCUAUUACGAAG- -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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