miRNA: 3'- -CCGca----AGACCUCUCG-AGUuuUCCGua -5'
miRNA: 3'- ccgCAAGACCUCUC-GAGUUUu--CC-GUa -5'
miRNA: 3'- -CCgca-AGACCUCUCG--AGUUUUC-CGUA- -5'
miRNA: 3'- -CCGCA-----AGACCUCu---------CGAGUuuUCCGua -5'
miRNA: 3'- -CCGCaaGaCCU-CUCGAGUUUUCCGUA- -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 | |||||||
| 28572 | 5' | -51.7 | NC_005946.1 | + | 81484 | 0.66 | 0.94543 |
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Target: 5'- aGGCagaggaUCUGGAGAGCaUCA--AGGCc- -3' miRNA: 3'- -CCGca----AGACCUCUCG-AGUuuUCCGua -5' |
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| 28572 | 5' | -51.7 | NC_005946.1 | + | 75640 | 0.67 | 0.940567 |
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Target: 5'- --gGUUCUGGAGGGuCUCGAGuuuGGaCAg -3' miRNA: 3'- ccgCAAGACCUCUC-GAGUUUu--CC-GUa -5' |
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| 28572 | 5' | -51.7 | NC_005946.1 | + | 86874 | 0.67 | 0.918384 |
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Target: 5'- aGGacugUCUGGGGAGCagUCAGGGGaGCGUc -3' miRNA: 3'- -CCgca-AGACCUCUCG--AGUUUUC-CGUA- -5' |
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| 28572 | 5' | -51.7 | NC_005946.1 | + | 56455 | 0.67 | 0.918384 |
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Target: 5'- gGGCGUggaccUCUGGAGucgaugggguGCUCAu-GGGCu- -3' miRNA: 3'- -CCGCA-----AGACCUCu---------CGAGUuuUCCGua -5' |
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| 28572 | 5' | -51.7 | NC_005946.1 | + | 8090 | 0.75 | 0.554085 |
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Target: 5'- gGGUGgcCaGGAuGAGCUCGGGAGGCAUc -3' miRNA: 3'- -CCGCaaGaCCU-CUCGAGUUUUCCGUA- -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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