miRNA: 3'- uuACUCa--GACCuuCGCGCCGa-CUGGg -5'
miRNA: 3'- uuaCUCAGAcc----UUCGCGCCgACUGGg -5'
miRNA: 3'- -UUACUCAGAccUUCGCG----------CCGACUGGg -5'
miRNA: 3'- uuaCUCaGACCu---UCGCG--CCG--ACUGGG- -5'
miRNA: 3'- -UUACUCAGACCUUCGCGCCGACUGGG- -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 | |||||||
| 22395 | 5' | -55.9 | NC_005056.1 | + | 28377 | 0.66 | 0.511282 |
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Target: 5'- -uUGAGgcgCUGGc-GCGUGGCgcGACCg -3' miRNA: 3'- uuACUCa--GACCuuCGCGCCGa-CUGGg -5' |
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| 22395 | 5' | -55.9 | NC_005056.1 | + | 5878 | 0.66 | 0.511282 |
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Target: 5'- --cGGGUCUuacgcaGGGCGCGGgUGGCCg -3' miRNA: 3'- uuaCUCAGAcc----UUCGCGCCgACUGGg -5' |
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| 22395 | 5' | -55.9 | NC_005056.1 | + | 8910 | 0.66 | 0.489585 |
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Target: 5'- gAAUGAGUUU--AAGCGUuuugaagaccGGCUGACCg -3' miRNA: 3'- -UUACUCAGAccUUCGCG----------CCGACUGGg -5' |
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| 22395 | 5' | -55.9 | NC_005056.1 | + | 12754 | 0.67 | 0.447555 |
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Target: 5'- --cGAG-CUGGcggcGGCGCugGGCaaUGACCCg -3' miRNA: 3'- uuaCUCaGACCu---UCGCG--CCG--ACUGGG- -5' |
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| 22395 | 5' | -55.9 | NC_005056.1 | + | 2845 | 1.1 | 0.000305 |
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Target: 5'- aAAUGAGUCUGGAAGCGCGGCUGACCCa -3' miRNA: 3'- -UUACUCAGACCUUCGCGCCGACUGGG- -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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