miRNA: 3'- aGCa-CCCCACCCUgCag-UUGCGUCuc -5'
miRNA: 3'- aGCACCCCA-CCCU-----GCAGUUGCgu-CUc -5'
miRNA: 3'- aGCACCCCa---CCCugC-AgUUgCGUCUC- -5'
miRNA: 3'- -AGCACCCCACCCUGCAGUUGCGUCUC- -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 | |||||||
| 465 | 5' | -56.9 | AC_000013.1 | + | 13452 | 0.66 | 0.552059 |
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Target: 5'- gCGgaGGGGUGGGAgGgcgGACGCGGu- -3' miRNA: 3'- aGCa-CCCCACCCUgCag-UUGCGUCuc -5' |
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| 465 | 5' | -56.9 | AC_000013.1 | + | 18015 | 0.69 | 0.429547 |
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Target: 5'- gCGUGGGGUcGGGAuucguCGUCGACGguuGAc -3' miRNA: 3'- aGCACCCCA-CCCU-----GCAGUUGCgu-CUc -5' |
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| 465 | 5' | -56.9 | AC_000013.1 | + | 9144 | 0.72 | 0.286767 |
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Target: 5'- cCGUGGGGcaugGGGugGgUgAGgGCGGAGg -3' miRNA: 3'- aGCACCCCa---CCCugC-AgUUgCGUCUC- -5' |
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| 465 | 5' | -56.9 | AC_000013.1 | + | 11681 | 1.08 | 0.00066 |
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Target: 5'- aUCGUGGGGUGGGACGUCAACGCAGAGc -3' miRNA: 3'- -AGCACCCCACCCUGCAGUUGCGUCUC- -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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