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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 | |||||||
| 28440 | 5' | -55.6 | NC_005946.1 | + | 22940 | 0.66 | 0.871277 |
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Target: 5'- aGGGuucCUG-GugGGAUCCCUGcaaaaGGCCu -3' miRNA: 3'- -CCUgu-GACaCugCCUAGGGAC-----UCGGu -5' |
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| 28440 | 5' | -55.6 | NC_005946.1 | + | 56390 | 0.66 | 0.863648 |
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Target: 5'- aGGcCGuCUGUGACGGccgaGUCCagGAGCCc -3' miRNA: 3'- -CCuGU-GACACUGCC----UAGGgaCUCGGu -5' |
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| 28440 | 5' | -55.6 | NC_005946.1 | + | 71777 | 0.66 | 0.847741 |
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Target: 5'- cGGGCACgGUccugGugGGGaaggugucucacUCCCUgGGGCCGg -3' miRNA: 3'- -CCUGUGaCA----CugCCU------------AGGGA-CUCGGU- -5' |
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| 28440 | 5' | -55.6 | NC_005946.1 | + | 659 | 0.66 | 0.836958 |
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Target: 5'- uGGACACccagcagcacaucuUGuUGAcgucuaccuCGGAUgCCUGAGCCu -3' miRNA: 3'- -CCUGUG--------------AC-ACU---------GCCUAgGGACUCGGu -5' |
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| 28440 | 5' | -55.6 | NC_005946.1 | + | 61840 | 0.67 | 0.821486 |
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Target: 5'- gGGACcuguaUGUGACGGGUCCggcuucgCUGAGaaaCAg -3' miRNA: 3'- -CCUGug---ACACUGCCUAGG-------GACUCg--GU- -5' |
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| 28440 | 5' | -55.6 | NC_005946.1 | + | 73530 | 0.68 | 0.776559 |
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Target: 5'- aGGACcCcGUGGCGGAUCU---GGCCAa -3' miRNA: 3'- -CCUGuGaCACUGCCUAGGgacUCGGU- -5' |
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| 28440 | 5' | -55.6 | NC_005946.1 | + | 55226 | 0.68 | 0.747377 |
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Target: 5'- aGGACACUGUc----GUCUCUGAGCCu -3' miRNA: 3'- -CCUGUGACAcugccUAGGGACUCGGu -5' |
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| 28440 | 5' | -55.6 | NC_005946.1 | + | 92092 | 1.1 | 0.001801 |
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Target: 5'- uGGACACUGUGACGGAUCCCUGAGCCAc -3' miRNA: 3'- -CCUGUGACACUGCCUAGGGACUCGGU- -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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