miRNA: 3'- aUGUUGCACCAGG--------CGGuGACCCUcca -5'
miRNA: 3'- aUGuUGCA------CCAG-GCGGUGA-CCCUCCa -5'
miRNA: 3'- aUGuuGcACCAGGCGGugA--CCCUCCA- -5'
miRNA: 3'- aUGUUGCACCa---GGCGGUGACC-----------CUCCa -5'
miRNA: 3'- -AUGUUGCACCAGGCGGUGACCCUCCA- -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 | |||||||
| 31853 | 5' | -58 | NC_006938.1 | + | 8629 | 0.66 | 0.556392 |
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Target: 5'- cAUGACGUGGUCCcacuggcuGCC-CUGGGAc-- -3' miRNA: 3'- aUGUUGCACCAGG--------CGGuGACCCUcca -5' |
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| 31853 | 5' | -58 | NC_006938.1 | + | 3588 | 0.69 | 0.398413 |
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Target: 5'- gGCcGCGUcgaucuGGUCgUGCCACUcGGGAGGg -3' miRNA: 3'- aUGuUGCA------CCAG-GCGGUGA-CCCUCCa -5' |
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| 31853 | 5' | -58 | NC_006938.1 | + | 31693 | 0.69 | 0.389504 |
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Target: 5'- aACuuCuUGGUCCGCUugUcaGGGAGGUc -3' miRNA: 3'- aUGuuGcACCAGGCGGugA--CCCUCCA- -5' |
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| 31853 | 5' | -58 | NC_006938.1 | + | 63087 | 0.73 | 0.246123 |
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Target: 5'- gGCAACGUGGgcugUCGCCGCUGGaauacggcaguGGGGc -3' miRNA: 3'- aUGUUGCACCa---GGCGGUGACC-----------CUCCa -5' |
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| 31853 | 5' | -58 | NC_006938.1 | + | 31748 | 1.05 | 0.001167 |
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Target: 5'- uUACAACGUGGUCCGCCACUGGGAGGUc -3' miRNA: 3'- -AUGUUGCACCAGGCGGUGACCCUCCA- -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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