miRNA: 3'- -CC-GACUaa----CACUACGGCCAUca----GUCU- -5'
miRNA: 3'- -CCGACUaa-CACUa-CGGCCAu---CAGUCU- -5'
miRNA: 3'- -CCGACuaaCACU--------------ACGGCCA----------UCAGUCU- -5'
miRNA: 3'- -CCGACUAACACUACGGCCAUCAGUCU- -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 | |||||||
| 25997 | 5' | -50.9 | NC_005340.1 | + | 6406 | 0.67 | 0.699794 |
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Target: 5'- cGGcCUGAcccugcGUGAUGCCGGUAugaauaCAGAg -3' miRNA: 3'- -CC-GACUaa----CACUACGGCCAUca----GUCU- -5' |
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| 25997 | 5' | -50.9 | NC_005340.1 | + | 6753 | 0.69 | 0.593482 |
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Target: 5'- aGGUUGGgcgGUGGacGCCGGUcgcuGUCAGGg -3' miRNA: 3'- -CCGACUaa-CACUa-CGGCCAu---CAGUCU- -5' |
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| 25997 | 5' | -50.9 | NC_005340.1 | + | 12251 | 0.74 | 0.354981 |
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Target: 5'- uGGCUGuugGUGAcggcgguggaaaacUGCCGGUgccugaugccGGUCAGAc -3' miRNA: 3'- -CCGACuaaCACU--------------ACGGCCA----------UCAGUCU- -5' |
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| 25997 | 5' | -50.9 | NC_005340.1 | + | 28845 | 1.12 | 0.00077 |
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Target: 5'- cGGCUGAUUGUGAUGCCGGUAGUCAGAu -3' miRNA: 3'- -CCGACUAACACUACGGCCAUCAGUCU- -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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