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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 | |||||||
| 459 | 3' | -48.9 | AC_000013.1 | + | 10845 | 0.68 | 0.858513 |
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Target: 5'- --cGUGCgcga-GACGCCCUCggaaGCGGa -3' miRNA: 3'- uuuUACGauucgUUGCGGGAGa---UGCC- -5' |
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| 459 | 3' | -48.9 | AC_000013.1 | + | 5001 | 0.7 | 0.735346 |
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Target: 5'- uGAGAUcGgUGAGCGAUGCCgUCU-CGGa -3' miRNA: 3'- -UUUUA-CgAUUCGUUGCGGgAGAuGCC- -5' |
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| 459 | 3' | -48.9 | AC_000013.1 | + | 18586 | 0.7 | 0.735346 |
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Target: 5'- ---uUGaCUGAGCGGCGCgUUCgACGGg -3' miRNA: 3'- uuuuAC-GAUUCGUUGCGgGAGaUGCC- -5' |
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| 459 | 3' | -48.9 | AC_000013.1 | + | 24134 | 0.72 | 0.64218 |
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Target: 5'- ----aGCUGcGGCAugGCCUUCU-CGGa -3' miRNA: 3'- uuuuaCGAU-UCGUugCGGGAGAuGCC- -5' |
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| 459 | 3' | -48.9 | AC_000013.1 | + | 28521 | 0.72 | 0.626798 |
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Target: 5'- gAGGAUGCgGAGCGGCGuuuucgagaugcccCCCUCgACGGa -3' miRNA: 3'- -UUUUACGaUUCGUUGC--------------GGGAGaUGCC- -5' |
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| 459 | 3' | -48.9 | AC_000013.1 | + | 18722 | 0.73 | 0.583155 |
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Target: 5'- ---cUGCUcaAAGCGGCGCaCCcgCUACGGc -3' miRNA: 3'- uuuuACGA--UUCGUUGCG-GGa-GAUGCC- -5' |
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| 459 | 3' | -48.9 | AC_000013.1 | + | 8786 | 1.08 | 0.003346 |
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Target: 5'- gAAAAUGCUAAGCAACGCCCUCUACGGc -3' miRNA: 3'- -UUUUACGAUUCGUUGCGGGAGAUGCC- -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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