miRNA: 3'- aGCCGUGGUa---------GUUGGGG--UAU-GCCCGC- -5'
miRNA: 3'- aGCCGUGGUAGuuGGGGUAuGCC--CGC- -5'
miRNA: 3'- -AGCCGUGGUAGUUGGGGUAUGCCCGC- -5'
Results 1 - 3 of 3 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 | |||||||
| 31991 | 3' | -56.9 | NC_006949.1 | + | 4773 | 0.66 | 0.59762 |
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Target: 5'- gCGGUGCCAgggugccuucCAGCCCUuuAUAgUGGGCGu -3' miRNA: 3'- aGCCGUGGUa---------GUUGGGG--UAU-GCCCGC- -5' |
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| 31991 | 3' | -56.9 | NC_006949.1 | + | 39249 | 0.71 | 0.318099 |
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Target: 5'- cCGGCGCUAUCugUCCCGUuCGGugGCGg -3' miRNA: 3'- aGCCGUGGUAGuuGGGGUAuGCC--CGC- -5' |
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| 31991 | 3' | -56.9 | NC_006949.1 | + | 2433 | 1.08 | 0.000661 |
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Target: 5'- gUCGGCACCAUCAACCCCAUACGGGCGc -3' miRNA: 3'- -AGCCGUGGUAGUUGGGGUAUGCCCGC- -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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