miRNA: 3'- -ACGaaUUCAGCUa-CGCGG--AC--------UUCGUC- -5'
miRNA: 3'- -ACGAaUUCaGCUACGCGGa---CuuCGUC- -5'
miRNA: 3'- aCGaa-UUCaGCUA-------CGCGG-ACUUCGUC- -5'
miRNA: 3'- -ACGAAUUCAGCUACGCGGACUUCGUC- -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 | |||||||
| 28082 | 3' | -51 | NC_005887.1 | + | 1082 | 0.68 | 0.729436 |
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Target: 5'- gUGCgcAGGUCGAcgGCGCCauUGccgacgccGAGCAGg -3' miRNA: 3'- -ACGaaUUCAGCUa-CGCGG--AC--------UUCGUC- -5' |
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| 28082 | 3' | -51 | NC_005887.1 | + | 28918 | 0.68 | 0.71811 |
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Target: 5'- gUGCU-GAG-CGGUGCGCCgcucGucGCAGc -3' miRNA: 3'- -ACGAaUUCaGCUACGCGGa---CuuCGUC- -5' |
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| 28082 | 3' | -51 | NC_005887.1 | + | 13760 | 0.69 | 0.682445 |
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Target: 5'- gGCgcgAGGaCGAUuuccagaGCGCCgUGAAGCAGg -3' miRNA: 3'- aCGaa-UUCaGCUA-------CGCGG-ACUUCGUC- -5' |
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| 28082 | 3' | -51 | NC_005887.1 | + | 7073 | 1.1 | 0.001337 |
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Target: 5'- cUGCUUAAGUCGAUGCGCCUGAAGCAGg -3' miRNA: 3'- -ACGAAUUCAGCUACGCGGACUUCGUC- -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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