miRNA: 3'- -UGUCaGCCCCC-GCU----------CCUGGA----CCAACA- -5'
miRNA: 3'- -UGUCaGCCc-----CCGCUC-CUGGACCAACa -5'
miRNA: 3'- -UGUCAGCC--CCCGCUcCUGGACCaa-CA- -5'
miRNA: 3'- -UGUCAGCCCCCGCUCCUGGACCAACA- -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 | |||||||
| 23144 | 5' | -59.6 | NC_005178.1 | + | 29693 | 0.68 | 0.274281 |
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Target: 5'- cACGGaCGGGGGaCGGaugcgccacuGGACCUcgccGGUUGUg -3' miRNA: 3'- -UGUCaGCCCCC-GCU----------CCUGGA----CCAACA- -5' |
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| 23144 | 5' | -59.6 | NC_005178.1 | + | 12658 | 0.7 | 0.211467 |
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Target: 5'- gGCGGcCGGcgcgcuGGCGGGuGGCCUGGUUGc -3' miRNA: 3'- -UGUCaGCCc-----CCGCUC-CUGGACCAACa -5' |
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| 23144 | 5' | -59.6 | NC_005178.1 | + | 33094 | 0.73 | 0.118935 |
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Target: 5'- aGCGGUCGGcaGGGUGAaGACCUGGgcgGUg -3' miRNA: 3'- -UGUCAGCC--CCCGCUcCUGGACCaa-CA- -5' |
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| 23144 | 5' | -59.6 | NC_005178.1 | + | 24699 | 1.06 | 0.000367 |
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Target: 5'- gACAGUCGGGGGCGAGGACCUGGUUGUc -3' miRNA: 3'- -UGUCAGCCCCCGCUCCUGGACCAACA- -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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