miRNA: 3'- aaAGaa--GCAGUGGCUC-GuGUA-GCGGU- -5'
miRNA: 3'- aaaGAaGC-AGUGGC--------------UCGUGUAGCGGU- -5'
miRNA: 3'- aaaGAAGCAGugGC--UCGUGU----AGCGGu -5'
miRNA: 3'- aaagaAGCAG---UGGCUCGugUAgCGGU- -5'
miRNA: 3'- -AAAGAAGCAGUGGCUCGUGUAGCGGU- -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 | |||||||
| 666 | 5' | -52.8 | AC_000018.1 | + | 9384 | 0.66 | 0.669993 |
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Target: 5'- -gUCgugcCGUCACCGAGaC-CAUgCGCCGc -3' miRNA: 3'- aaAGaa--GCAGUGGCUC-GuGUA-GCGGU- -5' |
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| 666 | 5' | -52.8 | AC_000018.1 | + | 16058 | 0.66 | 0.6665 |
|
Target: 5'- --cCUaUGcUCGCCGgaagagccgaaggaGGCGCAUCGCCAg -3' miRNA: 3'- aaaGAaGC-AGUGGC--------------UCGUGUAGCGGU- -5' |
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| 666 | 5' | -52.8 | AC_000018.1 | + | 17620 | 0.68 | 0.576642 |
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Target: 5'- --cCUUCGUCugUGgcGGCGCAucccUCGCCc -3' miRNA: 3'- aaaGAAGCAGugGC--UCGUGU----AGCGGu -5' |
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| 666 | 5' | -52.8 | AC_000018.1 | + | 6919 | 0.68 | 0.565094 |
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Target: 5'- ----cUCGUCaccGCCGAGCugGUaGCCAa -3' miRNA: 3'- aaagaAGCAG---UGGCUCGugUAgCGGU- -5' |
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| 666 | 5' | -52.8 | AC_000018.1 | + | 9030 | 1.06 | 0.001347 |
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Target: 5'- aUUUCUUCGUCACCGAGCACAUCGCCAc -3' miRNA: 3'- -AAAGAAGCAGUGGCUCGUGUAGCGGU- -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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