miRNA: 3'- -CCCAAGCCUGGUuCGCgCa-UGaaGUC- -5'
miRNA: 3'- -CCCa--AGCCugGUUCGC-GCAu--GAAGUC- -5'
miRNA: 3'- -CCCaaGCCUGGUUCGCGcaugAAGUc -5'
miRNA: 3'- -CCCAAGCCUGGUUCGCGCAUGAAGUC- -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 | |||||||
| 19635 | 5' | -52.4 | NC_004686.1 | + | 22345 | 0.68 | 0.775099 |
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Target: 5'- cGGGUUCGGAUCG-GCGgGcgGCagCGGu -3' miRNA: 3'- -CCCAAGCCUGGUuCGCgCa-UGaaGUC- -5' |
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| 19635 | 5' | -52.4 | NC_004686.1 | + | 34422 | 0.7 | 0.690003 |
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Target: 5'- uGGGgcgUUGGugCGGGUGaCGUucuCUUCGGa -3' miRNA: 3'- -CCCa--AGCCugGUUCGC-GCAu--GAAGUC- -5' |
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| 19635 | 5' | -52.4 | NC_004686.1 | + | 29852 | 0.7 | 0.678986 |
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Target: 5'- gGGGggUGGGCCAGGCGCa---UUCGa -3' miRNA: 3'- -CCCaaGCCUGGUUCGCGcaugAAGUc -5' |
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| 19635 | 5' | -52.4 | NC_004686.1 | + | 6913 | 1.11 | 0.001643 |
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Target: 5'- cGGGUUCGGACCAAGCGCGUACUUCAGc -3' miRNA: 3'- -CCCAAGCCUGGUUCGCGCAUGAAGUC- -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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