miRNA: 3'- caagAUUUCGaa--CUG-CGUCGUGaCCG- -5'
miRNA: 3'- caagaUUUCGAACUGCg---UCGUG-ACCG- -5'
miRNA: 3'- caaGAUUUCGaac-----UGCGUCGUGACCG- -5'
miRNA: 3'- cAAGA----UUUCGaACUGCGUCGUga-CCG- -5'
miRNA: 3'- -CAAGAUUUCGAACUGCGUCGUGACCG- -5'
Results 1 - 5 of 5 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 | |||||||
| 669 | 5' | -49.3 | AC_000018.1 | + | 4469 | 0.66 | 0.871291 |
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Target: 5'- ---aUGGGGCcgugGGCaGCGGCACgGGCg -3' miRNA: 3'- caagAUUUCGaa--CUG-CGUCGUGaCCG- -5' |
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| 669 | 5' | -49.3 | AC_000018.1 | + | 6128 | 0.68 | 0.793673 |
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Target: 5'- ----aGAAGCUUGGCGauggAGCGCaUGGUu -3' miRNA: 3'- caagaUUUCGAACUGCg---UCGUG-ACCG- -5' |
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| 669 | 5' | -49.3 | AC_000018.1 | + | 10490 | 0.69 | 0.738217 |
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Target: 5'- --gCUGGAGCcgcagcuaACGUGGUACUGGCa -3' miRNA: 3'- caaGAUUUCGaac-----UGCGUCGUGACCG- -5' |
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| 669 | 5' | -49.3 | AC_000018.1 | + | 14194 | 0.72 | 0.53639 |
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Target: 5'- cUUCUuacgAGAGCgUGAUGCAGCAacaGGCg -3' miRNA: 3'- cAAGA----UUUCGaACUGCGUCGUga-CCG- -5' |
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| 669 | 5' | -49.3 | AC_000018.1 | + | 10658 | 1.12 | 0.001147 |
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Target: 5'- uGUUCUAAAGCUUGACGCAGCACUGGCu -3' miRNA: 3'- -CAAGAUUUCGAACUGCGUCGUGACCG- -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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