miRNA: 3'- -CUGAaCGGcuagAGCCGCCGCU------------GAGC- -5'
miRNA: 3'- cUGAA-CG-GCUA-GAGCCGCCGCUgAGC- -5'
miRNA: 3'- cugaaCGGCUAGaGCCGC-CGCUG-AGC- -5'
miRNA: 3'- cUGaACGGCUa--GAGCCGCCGCUga-Gc -5'
miRNA: 3'- -CUGaa-CGGCUAGAGcCGCC-GC-UGAGC- -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 | |||||||
| 8910 | 3' | -57.2 | NC_002484.1 | + | 875 | 0.66 | 0.61771 |
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Target: 5'- cGACUcGCCa---UCGGCGGCGAauagguaaaugcCUCGu -3' miRNA: 3'- -CUGAaCGGcuagAGCCGCCGCU------------GAGC- -5' |
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| 8910 | 3' | -57.2 | NC_002484.1 | + | 52305 | 0.68 | 0.511697 |
|
Target: 5'- aGCUUgGCgCGGUaCUCGGCGGUGA-UCGc -3' miRNA: 3'- cUGAA-CG-GCUA-GAGCCGCCGCUgAGC- -5' |
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| 8910 | 3' | -57.2 | NC_002484.1 | + | 36421 | 0.7 | 0.413958 |
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Target: 5'- ----aGCCGAUC-CGGCGuGUGACaUCGa -3' miRNA: 3'- cugaaCGGCUAGaGCCGC-CGCUG-AGC- -5' |
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| 8910 | 3' | -57.2 | NC_002484.1 | + | 28157 | 0.7 | 0.386937 |
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Target: 5'- aAC-UGCCGAcuaCUCGGCGGCGAaagCa -3' miRNA: 3'- cUGaACGGCUa--GAGCCGCCGCUga-Gc -5' |
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| 8910 | 3' | -57.2 | NC_002484.1 | + | 5008 | 0.71 | 0.336498 |
|
Target: 5'- uGACgaaGCCGGUCUC-GCGGaCGuACUCGa -3' miRNA: 3'- -CUGaa-CGGCUAGAGcCGCC-GC-UGAGC- -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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