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| ID | Location | Perfect MFE.* | RefSeq Acc. |
strand
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Start Position | R_P_ratio# | P value |
| Predicted miRNA align pattern | |||||||
| 31952 | 3' | -58.4 | NC_006943.1 | + | 5856 | 1.11 | 0.00001 |
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Target: 5'- uCAACACGGCCUCCCUCAAGCCACCCCa -3' miRNA: 3'- -GUUGUGCCGGAGGGAGUUCGGUGGGG- -5' |
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| 31952 | 3' | -58.4 | NC_006943.1 | + | 4024 | 0.75 | 0.014984 |
|
Target: 5'- gGACcCGGCCaaacucuuugccUCCCUUAAGCUGCUCCa -3' miRNA: 3'- gUUGuGCCGG------------AGGGAGUUCGGUGGGG- -5' |
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| 31952 | 3' | -58.4 | NC_006943.1 | + | 5043 | 0.75 | 0.016614 |
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Target: 5'- --cCACaGCCUCCCUCAcgggGGCCGCUaCCg -3' miRNA: 3'- guuGUGcCGGAGGGAGU----UCGGUGG-GG- -5' |
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| 31952 | 3' | -58.4 | NC_006943.1 | + | 2883 | 0.66 | 0.087633 |
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Target: 5'- gAGCGCGGa--CCC-CAGGCCAgaCCCa -3' miRNA: 3'- gUUGUGCCggaGGGaGUUCGGUg-GGG- -5' |
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| 31952 | 3' | -58.4 | NC_006943.1 | + | 5647 | 0.66 | 0.100005 |
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Target: 5'- -cACugGaGCCUCCC-----CCACCCCc -3' miRNA: 3'- guUGugC-CGGAGGGaguucGGUGGGG- -5' |
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| 31952 | 3' | -58.4 | NC_006943.1 | + | 5098 | 0.67 | 0.076725 |
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Target: 5'- --cCACGGCUuuggugccgUCCCgguAGCgGCCCCc -3' miRNA: 3'- guuGUGCCGG---------AGGGaguUCGgUGGGG- -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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