miRNA: 3'- -CC-GGGGUGaUACg------CCC-----UCCC-UGUUCG- -5'
miRNA: 3'- cCGG-GG------UGAUACGCCC--UCCCUGuuCG- -5'
miRNA: 3'- -CCGGGGUGauaCgCCCUCCCUguUCG- -5'
miRNA: 3'- -CCGGGGUGAUACGCCCUCCCUGUUCG- -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 | |||||||
| 84 | 3' | -57.6 | AC_000005.1 | + | 25694 | 0.66 | 0.471404 |
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Target: 5'- cGGaCCCCAC-AUGauuuccaGGGugaauGGGGuACGAGCc -3' miRNA: 3'- -CC-GGGGUGaUACg------CCC-----UCCC-UGUUCG- -5' |
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| 84 | 3' | -57.6 | AC_000005.1 | + | 31385 | 0.66 | 0.461199 |
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Target: 5'- uGCCgCUugagugACUGUGCGGGcgAGGGAUucGUu -3' miRNA: 3'- cCGG-GG------UGAUACGCCC--UCCCUGuuCG- -5' |
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| 84 | 3' | -57.6 | AC_000005.1 | + | 24265 | 0.67 | 0.41202 |
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Target: 5'- uGGCUCCACa--G-GGGAGGGG--GGCa -3' miRNA: 3'- -CCGGGGUGauaCgCCCUCCCUguUCG- -5' |
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| 84 | 3' | -57.6 | AC_000005.1 | + | 20116 | 1.13 | 0.000161 |
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Target: 5'- gGGCCCCACUAUGCGGGAGGGACAAGCu -3' miRNA: 3'- -CCGGGGUGAUACGCCCUCCCUGUUCG- -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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