miRNA: 3'- cAgGGCCaaCAGUGGUGGGG-------CGACUA- -5'
miRNA: 3'- -CAGGGCCaa-CAGUGG-UGGGgCGacua -5'
miRNA: 3'- caGGGCCaACAGUGGUGGGGCga-CUa -5'
miRNA: 3'- caGGGCCAACa---GU---GGUGGGGCGACUa -5'
miRNA: 3'- -CAGGGCCAACAGUGGUGGGGCGACUA- -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 | |||||||
| 18374 | 5' | -59.2 | NC_004681.1 | + | 50946 | 0.67 | 0.502433 |
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Target: 5'- uUgCCGGg-GUCGCCGCCCUcgccauuGCUGGUg -3' miRNA: 3'- cAgGGCCaaCAGUGGUGGGG-------CGACUA- -5' |
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| 18374 | 5' | -59.2 | NC_004681.1 | + | 35709 | 0.69 | 0.3737 |
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Target: 5'- uGUCCCGGgcgGUCACCgACCUgGCg--- -3' miRNA: 3'- -CAGGGCCaa-CAGUGG-UGGGgCGacua -5' |
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| 18374 | 5' | -59.2 | NC_004681.1 | + | 6263 | 0.72 | 0.268586 |
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Target: 5'- -cUCCGG-UGUCGCCACCCCGaacGAg -3' miRNA: 3'- caGGGCCaACAGUGGUGGGGCga-CUa -5' |
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| 18374 | 5' | -59.2 | NC_004681.1 | + | 25102 | 0.73 | 0.214486 |
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Target: 5'- -cCUCGGUUGgccgCGgacCCACCCCGCUGGa -3' miRNA: 3'- caGGGCCAACa---GU---GGUGGGGCGACUa -5' |
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| 18374 | 5' | -59.2 | NC_004681.1 | + | 9352 | 1.05 | 0.001111 |
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Target: 5'- cGUCCCGGUUGUCACCACCCCGCUGAUc -3' miRNA: 3'- -CAGGGCCAACAGUGGUGGGGCGACUA- -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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