miRNA: 3'- ugAUGCUUcACCUCGCUCGGGacuug -5'
miRNA: 3'- uGAUG-CUUCACCuCgCUCGGGa---CUUg -5'
miRNA: 3'- -UGAUGCUUC-ACCUCGC------------UCGG---------GACUUG- -5'
miRNA: 3'- -UGAUGCUUCACCUCGCUCGGGACUUG- -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 | |||||||
| 17502 | 3' | -54 | NC_004456.1 | + | 30531 | 0.67 | 0.633024 |
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Target: 5'- -gUGCGGA-UGGGGCGGGCCCc---- -3' miRNA: 3'- ugAUGCUUcACCUCGCUCGGGacuug -5' |
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| 17502 | 3' | -54 | NC_004456.1 | + | 26138 | 0.68 | 0.587512 |
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Target: 5'- cCUACgGGAGUGGuGgGAGCCUgacgGAAg -3' miRNA: 3'- uGAUG-CUUCACCuCgCUCGGGa---CUUg -5' |
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| 17502 | 3' | -54 | NC_004456.1 | + | 13928 | 0.74 | 0.27991 |
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Target: 5'- uGCUACGGAGaUGGAGCGccgucuggagguGGCCauugccccgCUGAGCg -3' miRNA: 3'- -UGAUGCUUC-ACCUCGC------------UCGG---------GACUUG- -5' |
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| 17502 | 3' | -54 | NC_004456.1 | + | 15814 | 1.1 | 0.000709 |
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Target: 5'- gACUACGAAGUGGAGCGAGCCCUGAACg -3' miRNA: 3'- -UGAUGCUUCACCUCGCUCGGGACUUG- -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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