miRNA: 3'- aACCCCCaaCUCC-GUCGGaug----CUCGG- -5'
miRNA: 3'- -AACCCc-CAACUCCgUCGGAUGCu-CGG- -5'
miRNA: 3'- aacCCCCaACUCCgUCGGAugCUCGg -5'
miRNA: 3'- aaCC-CCCAACUC-CgUCGGAug---------CUCGG- -5'
miRNA: 3'- -AACCCCCAACUCCGUCGGAUGCUCGG- -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
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| Predicted miRNA align pattern | |||||||
| 13040 | 3' | -58.7 | NC_003390.1 | + | 30761 | 0.66 | 0.461584 |
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Target: 5'- cUGGGGGccGAGGaUGGCUgaagcgaGAGCCc -3' miRNA: 3'- aACCCCCaaCUCC-GUCGGaug----CUCGG- -5' |
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| 13040 | 3' | -58.7 | NC_003390.1 | + | 28021 | 0.67 | 0.413103 |
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Target: 5'- cUUGGGaaGUUGAGGgAGCUUGCGcuGCUu -3' miRNA: 3'- -AACCCc-CAACUCCgUCGGAUGCu-CGG- -5' |
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| 13040 | 3' | -58.7 | NC_003390.1 | + | 38757 | 0.68 | 0.359267 |
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Target: 5'- --aGGGGcUGAGGgGGCUUugGGGUa -3' miRNA: 3'- aacCCCCaACUCCgUCGGAugCUCGg -5' |
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| 13040 | 3' | -58.7 | NC_003390.1 | + | 9124 | 0.69 | 0.286666 |
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Target: 5'- -aGGaGGGUUGAGaGgGGCCUugaagccucuaGAGCCg -3' miRNA: 3'- aaCC-CCCAACUC-CgUCGGAug---------CUCGG- -5' |
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| 13040 | 3' | -58.7 | NC_003390.1 | + | 33506 | 1.08 | 0.000354 |
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Target: 5'- aUUGGGGGUUGAGGCAGCCUACGAGCCc -3' miRNA: 3'- -AACCCCCAACUCCGUCGGAUGCUCGG- -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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