miRNA: 3'- -CCGaaaGAACGGC-UGCG--CCUUuu--CUG- -5'
miRNA: 3'- -CCGaaagaa-CGGCUGCGCCuuuuCUG- -5'
miRNA: 3'- -CCGAAAGAACG-----GCUGcGCCUuuuCUG- -5'
miRNA: 3'- ccgaaAGaa-CGGCUGCGC---CUUUUCUG- -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 | |||||||
| 12243 | 5' | -49.8 | NC_003309.1 | + | 6513 | 0.66 | 0.936639 |
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Target: 5'- cGGCcg-CUUGCCGcGCGCccGGGAucacGACg -3' miRNA: 3'- -CCGaaaGAACGGC-UGCG--CCUUuu--CUG- -5' |
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| 12243 | 5' | -49.8 | NC_003309.1 | + | 22485 | 0.66 | 0.935542 |
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Target: 5'- cGGCggccaccGCCGACGCGGc---GGCa -3' miRNA: 3'- -CCGaaagaa-CGGCUGCGCCuuuuCUG- -5' |
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| 12243 | 5' | -49.8 | NC_003309.1 | + | 9003 | 0.68 | 0.891144 |
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Target: 5'- aGGCUUUUUUGCgucuuCGAC-CGGAuc-GACa -3' miRNA: 3'- -CCGAAAGAACG-----GCUGcGCCUuuuCUG- -5' |
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| 12243 | 5' | -49.8 | NC_003309.1 | + | 36555 | 0.69 | 0.831817 |
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Target: 5'- ----gUCgcgGCCGGCGCGaucGAGAAGGCg -3' miRNA: 3'- ccgaaAGaa-CGGCUGCGC---CUUUUCUG- -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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