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miRNA: 3'- gUGGCGGCAAaaaaGGAC-GCU------------GCCUU- -5'
miRNA: 3'- -GUGGCGGCAaaaaAGGACGc------UGCCUU- -5'
miRNA: 3'- gUGGCGGCaaaaaAGGaCGCugCCuu -5'
miRNA: 3'- -GUGGCGGCAAAAAAGGACGCUGCCUU- -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#
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P value |
| Predicted miRNA align pattern | |||||||
| 1059 | 3' | -52.6 | NC_000929.1 | + | 18739 | 0.66 | 0.744112 |
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Target: 5'- aGCCGCCGUUga--CCUGaCGAaauacgucccggUGGAAa -3' miRNA: 3'- gUGGCGGCAAaaaaGGAC-GCU------------GCCUU- -5' |
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| 1059 | 3' | -52.6 | NC_000929.1 | + | 34349 | 0.67 | 0.664526 |
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Target: 5'- aUACCGCCGU----UCCUGUaauucacACGGAAc -3' miRNA: 3'- -GUGGCGGCAaaaaAGGACGc------UGCCUU- -5' |
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| 1059 | 3' | -52.6 | NC_000929.1 | + | 18421 | 0.68 | 0.61801 |
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Target: 5'- gGCCGCCGccg--UCCaGCGugGGu- -3' miRNA: 3'- gUGGCGGCaaaaaAGGaCGCugCCuu -5' |
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| 1059 | 3' | -52.6 | NC_000929.1 | + | 19066 | 1.06 | 0.001663 |
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Target: 5'- cCACCGCCGUUUUUUCCUGCGACGGAAu -3' miRNA: 3'- -GUGGCGGCAAAAAAGGACGCUGCCUU- -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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