miRNA: 3'- -UUGAGGUcuu-UCGCCG-AGGGG------UCGGU- -5'
miRNA: 3'- -UUGAGGUCUUUCgCCGAG-------GGGUCGgu -5'
miRNA: 3'- -UUGAGGuCuuUCGCCGAG-----GGGUCGgu -5'
miRNA: 3'- uuGAGGUCU--UUCGCCGAGg-----------GGUCGGu -5'
miRNA: 3'- -UUGAGGUCUUUCGCCGAGGGGUCGGU- -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 | |||||||
| 22455 | 3' | -58.6 | NC_005062.1 | + | 4729 | 0.66 | 0.138411 |
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Target: 5'- cAACUCCGaccuGGCGGUgUCCCCaaagcaGGCCGg -3' miRNA: 3'- -UUGAGGUcuu-UCGCCG-AGGGG------UCGGU- -5' |
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| 22455 | 3' | -58.6 | NC_005062.1 | + | 5606 | 0.67 | 0.11415 |
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Target: 5'- gGACUCUGGGAAG-GGCUCacucuuuCCCGGCg- -3' miRNA: 3'- -UUGAGGUCUUUCgCCGAG-------GGGUCGgu -5' |
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| 22455 | 3' | -58.6 | NC_005062.1 | + | 3973 | 0.7 | 0.066152 |
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Target: 5'- gGACUCCuGuuGGUGGCUCuaugaCCCAGCa- -3' miRNA: 3'- -UUGAGGuCuuUCGCCGAG-----GGGUCGgu -5' |
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| 22455 | 3' | -58.6 | NC_005062.1 | + | 4609 | 0.72 | 0.0388 |
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Target: 5'- -uCUCCGGAcaGAGCGGCUCagagcggggcagCCAGCCu -3' miRNA: 3'- uuGAGGUCU--UUCGCCGAGg-----------GGUCGGu -5' |
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| 22455 | 3' | -58.6 | NC_005062.1 | + | 9127 | 1.05 | 0.000056 |
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Target: 5'- aAACUCCAGAAAGCGGCUCCCCAGCCAc -3' miRNA: 3'- -UUGAGGUCUUUCGCCGAGGGGUCGGU- -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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