miRNA: 3'- uUGGGAAgu-GGU-GUGGGGUuu-CAAGu -5'
miRNA: 3'- uUGGGaAGUGGUGuGGGGU---UUCaaGU- -5'
miRNA: 3'- -UUG-GGaa-GUGGugUGGGGUUUCA--AGU- -5'
miRNA: 3'- uuGGGaa-GUGGUGUGG-GGUUUCAAGU- -5'
miRNA: 3'- -UUGGGAAGUGGUGUGGGGUUUCAAGU- -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 | |||||||
| 8478 | 3' | -52.1 | NC_002167.1 | + | 28163 | 0.66 | 0.780705 |
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Target: 5'- cACCCUUaauCCGcCGCCCCAuguGUUUg -3' miRNA: 3'- uUGGGAAgu-GGU-GUGGGGUuu-CAAGu -5' |
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| 8478 | 3' | -52.1 | NC_002167.1 | + | 30373 | 0.66 | 0.748202 |
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Target: 5'- uGCCCaUCGCCGC-CCCCGuuaGGGggUAa -3' miRNA: 3'- uUGGGaAGUGGUGuGGGGU---UUCaaGU- -5' |
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| 8478 | 3' | -52.1 | NC_002167.1 | + | 23079 | 0.67 | 0.7145 |
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Target: 5'- cAGCgCCgcgCACUugGCCUCAAGGUuaUCAa -3' miRNA: 3'- -UUG-GGaa-GUGGugUGGGGUUUCA--AGU- -5' |
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| 8478 | 3' | -52.1 | NC_002167.1 | + | 26470 | 0.76 | 0.231595 |
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Target: 5'- -uCCCaccUACCACACCaCCAAAGUUCAu -3' miRNA: 3'- uuGGGaa-GUGGUGUGG-GGUUUCAAGU- -5' |
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| 8478 | 3' | -52.1 | NC_002167.1 | + | 26519 | 1.06 | 0.001721 |
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Target: 5'- gAACCCUUCACCACACCCCAAAGUUCAc -3' miRNA: 3'- -UUGGGAAGUGGUGUGGGGUUUCAAGU- -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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