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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 | |||||||
| 23203 | 5' | -56.6 | NC_005259.1 | + | 8354 | 0.66 | 0.680956 |
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Target: 5'- --cUgCUGCCGguAUCGCUcGGCGGCGGc -3' miRNA: 3'- uuuAgGGCGGU--UAGCGGcCUGUCGCC- -5' |
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| 23203 | 5' | -56.6 | NC_005259.1 | + | 36486 | 0.66 | 0.680956 |
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Target: 5'- cGAUCUCG-CGGUCGaCGGGCAGCu- -3' miRNA: 3'- uUUAGGGCgGUUAGCgGCCUGUCGcc -5' |
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| 23203 | 5' | -56.6 | NC_005259.1 | + | 56235 | 0.66 | 0.691594 |
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Target: 5'- -cGUCgCCGCCGAccaCGuuGGGauCGGCGGc -3' miRNA: 3'- uuUAG-GGCGGUUa--GCggCCU--GUCGCC- -5' |
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| 23203 | 5' | -56.6 | NC_005259.1 | + | 47625 | 0.66 | 0.691594 |
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Target: 5'- --uUCuuGUC-GUCGCCgaGGGCAGCGa -3' miRNA: 3'- uuuAGggCGGuUAGCGG--CCUGUCGCc -5' |
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| 23203 | 5' | -56.6 | NC_005259.1 | + | 19376 | 0.66 | 0.691594 |
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Target: 5'- ---cCCCGCUGAUCaCCGGccccaacgGCAGCGu -3' miRNA: 3'- uuuaGGGCGGUUAGcGGCC--------UGUCGCc -5' |
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| 23203 | 5' | -56.6 | NC_005259.1 | + | 68537 | 0.66 | 0.702177 |
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Target: 5'- ---gCCCGCCAcgCGUCG-ACAuCGGg -3' miRNA: 3'- uuuaGGGCGGUuaGCGGCcUGUcGCC- -5' |
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| 23203 | 5' | -56.6 | NC_005259.1 | + | 5636 | 0.66 | 0.702177 |
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Target: 5'- cGGAUCgUGCCcggCGa-GGACGGCGGg -3' miRNA: 3'- -UUUAGgGCGGuuaGCggCCUGUCGCC- -5' |
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| 23203 | 5' | -56.6 | NC_005259.1 | + | 53259 | 0.66 | 0.712694 |
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Target: 5'- -cGUCgCCGCCGcuGUCGCCGGuGCcGCc- -3' miRNA: 3'- uuUAG-GGCGGU--UAGCGGCC-UGuCGcc -5' |
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| 23203 | 5' | -56.6 | NC_005259.1 | + | 34866 | 0.66 | 0.723136 |
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Target: 5'- -uGUCCuCGUCGGU-GCCGGACcGgGGu -3' miRNA: 3'- uuUAGG-GCGGUUAgCGGCCUGuCgCC- -5' |
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| 23203 | 5' | -56.6 | NC_005259.1 | + | 66632 | 0.66 | 0.723136 |
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Target: 5'- -cGUCCCugGCCAccgcucggauuGcUGCCGGuCGGCGGu -3' miRNA: 3'- uuUAGGG--CGGU-----------UaGCGGCCuGUCGCC- -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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