miRNA: 3'- -CCUGCGG--------------CCGacCCGGugaUCCGGGc -5'
miRNA: 3'- ccUGCG---GCCGaCCCGGUGaUCCG-GGc -5'
miRNA: 3'- -CCUGCGG-------CCGACC-----------CGGUGaUCCGGGC- -5'
miRNA: 3'- cCUG-CGGCCGACCCGgugaUCCG-----GGC- -5'
Results 21 - 24 of 24 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 | |||||||
| 28336 | 5' | -63.7 | NC_005946.1 | + | 20729 | 0.66 | 0.488691 |
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Target: 5'- uGGACGCCguggucaccagccuGGCc-GGCCucgAGGCCCu -3' miRNA: 3'- -CCUGCGG--------------CCGacCCGGugaUCCGGGc -5' |
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| 28336 | 5' | -63.7 | NC_005946.1 | + | 82810 | 0.66 | 0.491472 |
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Target: 5'- -cACGUguaCGGCaGGGCCGCcAGGCaCCu -3' miRNA: 3'- ccUGCG---GCCGaCCCGGUGaUCCG-GGc -5' |
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| 28336 | 5' | -63.7 | NC_005946.1 | + | 72757 | 0.66 | 0.499859 |
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Target: 5'- aGGGCGCUcccgccaGGCUGGcgugguccggcGCUGCgGGGUCCGc -3' miRNA: 3'- -CCUGCGG-------CCGACC-----------CGGUGaUCCGGGC- -5' |
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| 28336 | 5' | -63.7 | NC_005946.1 | + | 59709 | 0.66 | 0.500795 |
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Target: 5'- uGGCgGCCGGCUGGGCaa--GGGUaaaguCCGg -3' miRNA: 3'- cCUG-CGGCCGACCCGgugaUCCG-----GGC- -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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