miRNA: 3'- ugcAGCGAugCAGG---GAGGcACUGaGG- -5'
miRNA: 3'- -UGCAGCGAUG--CAG-GGAGGCaCuGAGG- -5'
miRNA: 3'- -UGCA-----GCGau---GCA-GGGAGGCACU---GAGG- -5'
miRNA: 3'- -UGCAGCGAUGCAGGGAGGCACUGAGG- -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 | |||||||
| 30308 | 3' | -56.1 | NC_006367.1 | + | 3913 | 0.67 | 0.118793 |
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Target: 5'- --uUCGCUugGUCCuggCUCCuUGACcCCg -3' miRNA: 3'- ugcAGCGAugCAGG---GAGGcACUGaGG- -5' |
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| 30308 | 3' | -56.1 | NC_006367.1 | + | 1422 | 0.69 | 0.076966 |
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Target: 5'- cACGUCGCUACcuGUCuUCUCUG-GuCUCCc -3' miRNA: 3'- -UGCAGCGAUG--CAG-GGAGGCaCuGAGG- -5' |
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| 30308 | 3' | -56.1 | NC_006367.1 | + | 4341 | 0.7 | 0.058671 |
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Target: 5'- gACGUguauaUGCgacuuCGUaCCCUCCGUGAugcCUCCa -3' miRNA: 3'- -UGCA-----GCGau---GCA-GGGAGGCACU---GAGG- -5' |
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| 30308 | 3' | -56.1 | NC_006367.1 | + | 1494 | 1.12 | 1.6e-05 |
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Target: 5'- aACGUCGCUACGUCCCUCCGUGACUCCg -3' miRNA: 3'- -UGCAGCGAUGCAGGGAGGCACUGAGG- -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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