miRNA: 3'- gguACUGCGUCGAGCg------CUGGG-CGCaa -5'
miRNA: 3'- -GGUac---UGCGUCgAGCGCUgGGCGCAa -5'
miRNA: 3'- gGUACUGCGUCGagCGCUG--GgCGCaa -5'
miRNA: 3'- -GGUACUGCGUCGAGCGCUGGGCGCAA- -5'
Results 1 - 4 of 4 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 | |||||||
| 317 | 5' | -58.2 | AC_000010.1 | + | 3810 | 0.66 | 0.43615 |
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Target: 5'- --uUGGCGCAGCUUGaggcguuGACCCaGCGc- -3' miRNA: 3'- gguACUGCGUCGAGCg------CUGGG-CGCaa -5' |
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| 317 | 5' | -58.2 | AC_000010.1 | + | 11186 | 0.66 | 0.407347 |
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Target: 5'- cCCGcuuuaACGCGGgUCGCGAgCUGCGUc -3' miRNA: 3'- -GGUac---UGCGUCgAGCGCUgGGCGCAa -5' |
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| 317 | 5' | -58.2 | AC_000010.1 | + | 13978 | 0.68 | 0.344987 |
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Target: 5'- gCGUGAUGCAGCagGCGGCggCgGCGg- -3' miRNA: 3'- gGUACUGCGUCGagCGCUG--GgCGCaa -5' |
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| 317 | 5' | -58.2 | AC_000010.1 | + | 11255 | 1.08 | 0.000351 |
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Target: 5'- aCCAUGACGCAGCUCGCGACCCGCGUUa -3' miRNA: 3'- -GGUACUGCGUCGAGCGCUGGGCGCAA- -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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