miRNA: 3'- cugCCGC----CCACCaa--GCGGUG----CUCCCG- -5'
miRNA: 3'- cugCCGCC-CACCAAGCGGUGcUC-CCg -5'
miRNA: 3'- -CUGCCGC--CCaCCAa--GCGGU------GCUCCCG- -5'
miRNA: 3'- -CUGCCGCCCACCAAGCGGUGCUCCCG- -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 | |||||||
| 30587 | 5' | -60.9 | NC_006549.1 | + | 58952 | 0.66 | 0.711518 |
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Target: 5'- --gGGCGcuacGGUGGagggCGCUACggugGAGGGCg -3' miRNA: 3'- cugCCGC----CCACCaa--GCGGUG----CUCCCG- -5' |
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| 30587 | 5' | -60.9 | NC_006549.1 | + | 87879 | 0.67 | 0.642931 |
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Target: 5'- --aGGCGGcGUGGUUUGCUACaAGuGGa -3' miRNA: 3'- cugCCGCC-CACCAAGCGGUGcUC-CCg -5' |
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| 30587 | 5' | -60.9 | NC_006549.1 | + | 60460 | 0.71 | 0.408902 |
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Target: 5'- cGACGGCGuuGGcGGUgugCGCCGauagcgUGGGGGCu -3' miRNA: 3'- -CUGCCGC--CCaCCAa--GCGGU------GCUCCCG- -5' |
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| 30587 | 5' | -60.9 | NC_006549.1 | + | 34022 | 1.11 | 0.000806 |
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Target: 5'- cGACGGCGGGUGGUUCGCCACGAGGGCu -3' miRNA: 3'- -CUGCCGCCCACCAAGCGGUGCUCCCG- -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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