miRNA: 3'- agGUCGU----------UAGCGGGGCCG-----CCAGCauu -5'
miRNA: 3'- -AGGUcGUUAGCGGGGCCGCCAGcauu -5'
miRNA: 3'- -AGGUCGUUAGCGGGGCCGCCAGCAUU- -5'
miRNA: 3'- -AGGUCGUUAGCGGGGCCGCCAGCAUU- -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 | |||||||
| 8696 | 5' | -58.7 | NC_002229.2 | + | 111937 | 0.66 | 0.805219 |
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Target: 5'- -aCAGUAgguaaaugucGUCGCCCUGGCgcaucGGUCGg-- -3' miRNA: 3'- agGUCGU----------UAGCGGGGCCG-----CCAGCauu -5' |
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| 8696 | 5' | -58.7 | NC_002229.2 | + | 99848 | 0.68 | 0.672539 |
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Target: 5'- uUCCGaUAAUUGUUCCGGCGGUCa--- -3' miRNA: 3'- -AGGUcGUUAGCGGGGCCGCCAGcauu -5' |
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| 8696 | 5' | -58.7 | NC_002229.2 | + | 148126 | 1.06 | 0.002828 |
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Target: 5'- uUCCAGCAAUCGCCCCGGCGGUCGUAAc -3' miRNA: 3'- -AGGUCGUUAGCGGGGCCGCCAGCAUU- -5' |
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| 8696 | 5' | -58.7 | NC_002229.2 | + | 164489 | 1.06 | 0.002828 |
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Target: 5'- uUCCAGCAAUCGCCCCGGCGGUCGUAAc -3' miRNA: 3'- -AGGUCGUUAGCGGGGCCGCCAGCAUU- -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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