miRNA: 3'- aaGCUAGUCCAGg-----AAGUGCg-CCAGGg -5'
miRNA: 3'- aAGCUaGUCCa-----------GGAAGU-GCGCCAGGG- -5'
miRNA: 3'- aAGCUAGUCCa--------------GGaAGUGCG-CCAGgg -5'
miRNA: 3'- aaGCUAGucCAGGaaGUGCGCCAGGG- -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 | |||||||
| 12272 | 3' | -55.4 | NC_003309.1 | + | 19748 | 0.66 | 0.701437 |
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Target: 5'- -gUGAUCAGGUCgaucggUUCGCGaaGGUCCg -3' miRNA: 3'- aaGCUAGUCCAGg-----AAGUGCg-CCAGGg -5' |
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| 12272 | 3' | -55.4 | NC_003309.1 | + | 52585 | 0.67 | 0.611532 |
|
Target: 5'- aUCGAgCAGGacggccaccgggCCUUUGcCGUGGUCCCc -3' miRNA: 3'- aAGCUaGUCCa-----------GGAAGU-GCGCCAGGG- -5' |
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| 12272 | 3' | -55.4 | NC_003309.1 | + | 30951 | 0.69 | 0.538661 |
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Target: 5'- gUCGAUCAGGgacacuugcgcaaggCCaUCACGCuGGUCa- -3' miRNA: 3'- aAGCUAGUCCa--------------GGaAGUGCG-CCAGgg -5' |
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| 12272 | 3' | -55.4 | NC_003309.1 | + | 53085 | 0.69 | 0.495518 |
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Target: 5'- -cUGAUCuuGUCC--CACGCGGUUCCg -3' miRNA: 3'- aaGCUAGucCAGGaaGUGCGCCAGGG- -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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