miRNA: 3'- aaACUCGCGGuUGC---ACCUCAa---AGGGG- -5'
miRNA: 3'- aAACuCGCGGUUG-CACCU--------------CaaAGGGG- -5'
miRNA: 3'- aAACUCGCGGUUGCac--CUCAAAGGGG- -5'
miRNA: 3'- -AAACUCGCGGUUGCACCUCAAAGGGG- -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 | |||||||
| 75 | 3' | -52.9 | AC_000005.1 | + | 22594 | 0.67 | 0.611371 |
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Target: 5'- -cUGAGCGCU-GCGgucUGGGGUgcgcUCCCUc -3' miRNA: 3'- aaACUCGCGGuUGC---ACCUCAa---AGGGG- -5' |
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| 75 | 3' | -52.9 | AC_000005.1 | + | 21376 | 0.71 | 0.400683 |
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Target: 5'- cUUGuGCGCCAGCuGUGGGgagaaaauuuugacGgcUCCCCc -3' miRNA: 3'- aAACuCGCGGUUG-CACCU--------------CaaAGGGG- -5' |
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| 75 | 3' | -52.9 | AC_000005.1 | + | 449 | 0.75 | 0.214277 |
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Target: 5'- cUUGAGUGCCAGCGagaaGAGUUUUCUCu -3' miRNA: 3'- aAACUCGCGGUUGCac--CUCAAAGGGG- -5' |
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| 75 | 3' | -52.9 | AC_000005.1 | + | 412 | 1.1 | 0.000655 |
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Target: 5'- cUUUGAGCGCCAACGUGGAGUUUCCCCg -3' miRNA: 3'- -AAACUCGCGGUUGCACCUCAAAGGGG- -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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