miRNA: 3'- aGCCGaa--CGCCuC-CAUUC---UCG-AGGGG- -5'
miRNA: 3'- -AGCCgaa----CGCC-UCCAU-----UCUCgAGGGG- -5'
miRNA: 3'- aGCCGaaCGCCUCca----UUCUCGAGgGG- -5'
miRNA: 3'- aGCCGaa---------CGCC-UCCa----UUCuCGAGGGG- -5'
Results 21 - 24 of 24 are showing below:
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| ID | Location | Perfect MFE.* | RefSeq Acc. | strand |
Start Position
|
R_P_ratio# | P value |
| Predicted miRNA align pattern | |||||||
| 2706 | 5' | -56.7 | NC_001491.2 | + | 146364 | 0.67 | 0.82266 |
|
Target: 5'- cCGGCcacgGCGGcGaGUGAGuccGGCcUCCCCg -3' miRNA: 3'- aGCCGaa--CGCCuC-CAUUC---UCG-AGGGG- -5' |
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| 2706 | 5' | -56.7 | NC_001491.2 | + | 146800 | 0.66 | 0.891311 |
|
Target: 5'- gUCGGagcccagGCGGuGGGUAgggucAGAG-UCCCCg -3' miRNA: 3'- -AGCCgaa----CGCC-UCCAU-----UCUCgAGGGG- -5' |
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| 2706 | 5' | -56.7 | NC_001491.2 | + | 147048 | 0.69 | 0.720701 |
|
Target: 5'- gCGGCc-GCGGAGccggagAAGGGCUCgCCg -3' miRNA: 3'- aGCCGaaCGCCUCca----UUCUCGAGgGG- -5' |
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| 2706 | 5' | -56.7 | NC_001491.2 | + | 147090 | 0.68 | 0.794642 |
|
Target: 5'- aCGGUgggccacagggGCGGcAGGgucugAAG-GCUCCCCu -3' miRNA: 3'- aGCCGaa---------CGCC-UCCa----UUCuCGAGGGG- -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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