miRNA: 3'- aaGGGGACCUC----AGu--CUUGGGu------GGUUG- -5'
miRNA: 3'- -AAGg--GgaCCUCa--GUCUUGGGUGGuUG- -5'
miRNA: 3'- -AAGGGGACCUCAGUCUUGGGUGGUUG- -5'
miRNA: 3'- -AAGGGGaCCUCaGUCu---------UGGGUGGUUg -5'
miRNA: 3'- aAGGGGACC-UCAGuCUUGGGUg--GUUG- -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 |
| Predicted miRNA align pattern | |||||||
| 10650 | 5' | -56.2 | NC_002702.1 | + | 5261 | 0.66 | 0.479475 |
|
Target: 5'- -gCCCCUGGAGauguUCuuuGAGCUCucuuccuCCAACu -3' miRNA: 3'- aaGGGGACCUC----AGu--CUUGGGu------GGUUG- -5' |
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| 10650 | 5' | -56.2 | NC_002702.1 | + | 10327 | 0.68 | 0.352104 |
|
Target: 5'- aUUCagaCgaGGAGgggCAGGGCCCGCCuGCg -3' miRNA: 3'- -AAGg--GgaCCUCa--GUCUUGGGUGGuUG- -5' |
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| 10650 | 5' | -56.2 | NC_002702.1 | + | 14475 | 1.08 | 0.000394 |
|
Target: 5'- uUUCCCCUGGAGUCAGAACCCACCAACg -3' miRNA: 3'- -AAGGGGACCUCAGUCUUGGGUGGUUG- -5' |
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| 10650 | 5' | -56.2 | NC_002702.1 | + | 14831 | 0.67 | 0.417697 |
|
Target: 5'- gUUCCCCcGGGGaCGGccuuucuuuuGCCCGCCAGg -3' miRNA: 3'- -AAGGGGaCCUCaGUCu---------UGGGUGGUUg -5' |
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| 10650 | 5' | -56.2 | NC_002702.1 | + | 15834 | 0.66 | 0.447996 |
|
Target: 5'- cUCCCUUGGcAGUC-GAGCCUGgaaCAGCa -3' miRNA: 3'- aAGGGGACC-UCAGuCUUGGGUg--GUUG- -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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