miRNA: 3'- -GGaAGCCCCaCAGcc-----UCCGGUCCUCU- -5'
miRNA: 3'- -GGaaGCCCCaCaGCCUCCGGuCCUCU- -5'
miRNA: 3'- ggaAGCCCCa--CAGCCUCCGGUCCUCU- -5'
miRNA: 3'- -GGAAGCCCCACAGCCUCCGGUCCUCU- -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 | |||||||
| 4271 | 5' | -59.2 | NC_001710.1 | + | 4981 | 0.69 | 0.085624 |
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Target: 5'- cCCaUUGGGG-GUCauccgauGGGCCGGGAGAc -3' miRNA: 3'- -GGaAGCCCCaCAGcc-----UCCGGUCCUCU- -5' |
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| 4271 | 5' | -59.2 | NC_001710.1 | + | 392 | 0.7 | 0.060367 |
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Target: 5'- aCCagUGGGG-GcCGGGGGCUuGGAGAg -3' miRNA: 3'- -GGaaGCCCCaCaGCCUCCGGuCCUCU- -5' |
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| 4271 | 5' | -59.2 | NC_001710.1 | + | 5784 | 0.76 | 0.019428 |
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Target: 5'- --aUUGGGGgccGUCGGAGGUUGGGAGGg -3' miRNA: 3'- ggaAGCCCCa--CAGCCUCCGGUCCUCU- -5' |
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| 4271 | 5' | -59.2 | NC_001710.1 | + | 6471 | 1.11 | 0.000024 |
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Target: 5'- aCCUUCGGGGUGUCGGAGGCCAGGAGAg -3' miRNA: 3'- -GGAAGCCCCACAGCCUCCGGUCCUCU- -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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