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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 | |||||||
| 623 | 5' | -56.6 | AC_000017.1 | + | 33256 | 0.66 | 0.437598 |
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Target: 5'- uAGgGCGgUGGUGCUGCAGcaGCgcgCGa -3' miRNA: 3'- -UCgCGUgACCGCGACGUCuaCGaa-GU- -5' |
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| 623 | 5' | -56.6 | AC_000017.1 | + | 16022 | 0.68 | 0.370213 |
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Target: 5'- cGCGCACUgGGUGUUGguCGGAgcGCUUCu -3' miRNA: 3'- uCGCGUGA-CCGCGAC--GUCUa-CGAAGu -5' |
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| 623 | 5' | -56.6 | AC_000017.1 | + | 8669 | 0.68 | 0.361182 |
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Target: 5'- cGCGCGCgGGCaGgaGCuGGUGCUgcgCAc -3' miRNA: 3'- uCGCGUGaCCG-CgaCGuCUACGAa--GU- -5' |
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| 623 | 5' | -56.6 | AC_000017.1 | + | 12343 | 0.68 | 0.352306 |
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Target: 5'- uGCGgGC-GGCGCUGCAGAgccaGCcgUCc -3' miRNA: 3'- uCGCgUGaCCGCGACGUCUa---CGa-AGu -5' |
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| 623 | 5' | -56.6 | AC_000017.1 | + | 1974 | 0.69 | 0.318365 |
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Target: 5'- gGGCGCGCUGcG-GCUGCuGuUGCUUUu -3' miRNA: 3'- -UCGCGUGAC-CgCGACGuCuACGAAGu -5' |
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| 623 | 5' | -56.6 | AC_000017.1 | + | 11952 | 0.74 | 0.139266 |
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Target: 5'- uGCGCA-UGGCGCUGaAGGUGCUUa- -3' miRNA: 3'- uCGCGUgACCGCGACgUCUACGAAgu -5' |
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| 623 | 5' | -56.6 | AC_000017.1 | + | 24450 | 1.08 | 0.000337 |
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Target: 5'- uAGCGCACUGGCGCUGCAGAUGCUUCAa -3' miRNA: 3'- -UCGCGUGACCGCGACGUCUACGAAGU- -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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