miRNA: 3'- -CGGAGAagCUgACgGAAUGCC----GGACG- -5'
miRNA: 3'- cGGAGAAGCUGaCGGaaUGC---CGGACG- -5'
miRNA: 3'- -CGGAGAAgCuGACGGAAUGCCGGaCG- -5'
miRNA: 3'- -CGGAG-AA-GCUg-------ACGGA---AUGC-CGGACG- -5'
miRNA: 3'- -CGGAGAAGCUGACGGAAUGCCGGACG- -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 | |||||||
| 12040 | 5' | -54.6 | NC_003298.1 | + | 5248 | 0.66 | 0.654206 |
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Target: 5'- cGCUUCUg-GAgUGgCUUGCGGuauuCCUGCc -3' miRNA: 3'- -CGGAGAagCUgACgGAAUGCC----GGACG- -5' |
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| 12040 | 5' | -54.6 | NC_003298.1 | + | 19232 | 0.66 | 0.64286 |
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Target: 5'- aUCUCUUCGGCgGUCacACGuucGCCUGUg -3' miRNA: 3'- cGGAGAAGCUGaCGGaaUGC---CGGACG- -5' |
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| 12040 | 5' | -54.6 | NC_003298.1 | + | 16483 | 0.66 | 0.631503 |
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Target: 5'- gGUUUCUUgG-UUGCCUUGCGGUUaGCc -3' miRNA: 3'- -CGGAGAAgCuGACGGAAUGCCGGaCG- -5' |
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| 12040 | 5' | -54.6 | NC_003298.1 | + | 33360 | 0.66 | 0.620147 |
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Target: 5'- aGCCUCaUUaCGGaacuguagUGCCUcauUACGcGCCUGCc -3' miRNA: 3'- -CGGAG-AA-GCUg-------ACGGA---AUGC-CGGACG- -5' |
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| 12040 | 5' | -54.6 | NC_003298.1 | + | 11349 | 1.14 | 0.000297 |
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Target: 5'- gGCCUCUUCGACUGCCUUACGGCCUGCg -3' miRNA: 3'- -CGGAGAAGCUGACGGAAUGCCGGACG- -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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