miRNA: 3'- aCGCAgGUCACugCGGc-------GGCG-AGUUA- -5'
miRNA: 3'- aCGcaGGUCACu------GCGGCGGCGAGUua -5'
miRNA: 3'- aCGCA---------GGUCA-CUGCGGCgGCGAGUUA- -5'
miRNA: 3'- -ACGCAGGUCACUGCGGCGGCGAGUUA- -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 | |||||||
| 12729 | 5' | -58.6 | NC_003356.1 | + | 34363 | 0.66 | 0.415639 |
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Target: 5'- cGCGUgCGGUGugGCCcacagauuCCGCaUCGGUu -3' miRNA: 3'- aCGCAgGUCACugCGGc-------GGCG-AGUUA- -5' |
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| 12729 | 5' | -58.6 | NC_003356.1 | + | 20762 | 0.68 | 0.335984 |
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Target: 5'- cGCuaCCAGUGcccauuuCGCCGCCGUUCGc- -3' miRNA: 3'- aCGcaGGUCACu------GCGGCGGCGAGUua -5' |
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| 12729 | 5' | -58.6 | NC_003356.1 | + | 38433 | 0.7 | 0.223244 |
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Target: 5'- gGCGUgugacguugCCGGUgGAUGCCGgUGCUCAGUg -3' miRNA: 3'- aCGCA---------GGUCA-CUGCGGCgGCGAGUUA- -5' |
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| 12729 | 5' | -58.6 | NC_003356.1 | + | 28584 | 1.06 | 0.000489 |
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Target: 5'- cUGCGUCCAGUGACGCCGCCGCUCAAUa -3' miRNA: 3'- -ACGCAGGUCACUGCGGCGGCGAGUUA- -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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