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miRNA: 3'- -GGCGaC-UGGGG-CGGUC---CGCcACCCCa -5'
miRNA: 3'- -GGCGAC--------------UGG-GGCG-----GUCCGCcACCCCA- -5'
miRNA: 3'- -GGCGaCUGGGGCGGUCCGCcACC---CCA- -5'
miRNA: 3'- -GGCGACUGGGGCGGUCCGCCACCCCA- -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#
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P value |
| Predicted miRNA align pattern | |||||||
| 30539 | 5' | -65.2 | NC_006548.1 | + | 9406 | 0.66 | 0.199582 |
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Target: 5'- gCCGCaGcACCCCuGCCAGaucGCGaUGGGGc -3' miRNA: 3'- -GGCGaC-UGGGG-CGGUC---CGCcACCCCa -5' |
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| 30539 | 5' | -65.2 | NC_006548.1 | + | 34370 | 0.7 | 0.102233 |
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Target: 5'- aCCGCUGucccauucgacguaGCCgCCGCggaacCAGGCGuUGGGGUa -3' miRNA: 3'- -GGCGAC--------------UGG-GGCG-----GUCCGCcACCCCA- -5' |
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| 30539 | 5' | -65.2 | NC_006548.1 | + | 30761 | 0.73 | 0.057861 |
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Target: 5'- uCCGC-GAUCCCGCCGGGCGcUGGcucGGUu -3' miRNA: 3'- -GGCGaCUGGGGCGGUCCGCcACC---CCA- -5' |
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| 30539 | 5' | -65.2 | NC_006548.1 | + | 23537 | 1.07 | 0.000103 |
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Target: 5'- cCCGCUGACCCCGCCAGGCGGUGGGGUu -3' miRNA: 3'- -GGCGACUGGGGCGGUCCGCCACCCCA- -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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