miRNA: 3'- -GGCG-C-CCUC-GAGGU--CUGGUACCU--GUC- -5'
miRNA: 3'- gGC-GCCCU----CG-AgGUCUGGUACCUGUc -5'
miRNA: 3'- ggCgCCCUCGAGGUCUGGua----------CCUGUC- -5'
miRNA: 3'- -GGCGCCCUCGAGGUCUGGUACCUGUC- -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 | |||||||
| 222 | 5' | -58.3 | AC_000008.1 | + | 18318 | 0.68 | 0.330482 |
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Target: 5'- cCCGUaGaGGAGcCUCCAccGGCCGUGGAgaCAGu -3' miRNA: 3'- -GGCG-C-CCUC-GAGGU--CUGGUACCU--GUC- -5' |
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| 222 | 5' | -58.3 | AC_000008.1 | + | 17148 | 0.7 | 0.256925 |
|
Target: 5'- gCGcCGGGAcuggGCgUgCAGACCGUGGACGu -3' miRNA: 3'- gGC-GCCCU----CG-AgGUCUGGUACCUGUc -5' |
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| 222 | 5' | -58.3 | AC_000008.1 | + | 8609 | 0.76 | 0.08929 |
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Target: 5'- -aGgGGGGGCUCCGGACCcgccgggagaggGGGCAGg -3' miRNA: 3'- ggCgCCCUCGAGGUCUGGua----------CCUGUC- -5' |
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| 222 | 5' | -58.3 | AC_000008.1 | + | 27526 | 1.09 | 0.000302 |
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Target: 5'- gCCGCGGGAGCUCCAGACCAUGGACAGc -3' miRNA: 3'- -GGCGCCCUCGAGGUCUGGUACCUGUC- -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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