miRNA: 3'- -CCaACGGUC--------------GACG-CGCgCGUGGAGUa -5'
miRNA: 3'- cCAACGGU-CGA--CGCGCGCGUGGa-GUa -5'
miRNA: 3'- ccaACGGUCGaCGCGCGcG-UGGAGUa -5'
miRNA: 3'- cCAACGG----UCgACGCGCGCGUgGAgUa -5'
miRNA: 3'- -CCAACGGUCGACGCGCGCGUGGAGUA- -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 | |||||||
| 14661 | 5' | -59 | NC_003525.1 | + | 51477 | 0.66 | 0.479063 |
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Target: 5'- gGGaUGCCGGacauuaccggacaaCUGCuGCG-GCACCUCAa -3' miRNA: 3'- -CCaACGGUC--------------GACG-CGCgCGUGGAGUa -5' |
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| 14661 | 5' | -59 | NC_003525.1 | + | 48364 | 0.67 | 0.414521 |
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Target: 5'- cGUUGUCAuGCUugGCGUGCGUACCagCAa -3' miRNA: 3'- cCAACGGU-CGA--CGCGCGCGUGGa-GUa -5' |
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| 14661 | 5' | -59 | NC_003525.1 | + | 35838 | 0.68 | 0.396312 |
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Target: 5'- --aUGCCAGCgGCGCGCuCgGCUUCAc -3' miRNA: 3'- ccaACGGUCGaCGCGCGcG-UGGAGUa -5' |
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| 14661 | 5' | -59 | NC_003525.1 | + | 20076 | 0.7 | 0.298419 |
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Target: 5'- uGUUGCCgaugAGgUGCGCGCGCAgCUgGc -3' miRNA: 3'- cCAACGG----UCgACGCGCGCGUgGAgUa -5' |
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| 14661 | 5' | -59 | NC_003525.1 | + | 20171 | 1.07 | 0.000543 |
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Target: 5'- cGGUUGCCAGCUGCGCGCGCACCUCAUc -3' miRNA: 3'- -CCAACGGUCGACGCGCGCGUGGAGUA- -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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