miRNA: 3'- -UGGGGCgGCCGaa--GUaAGCUUGGGUC- -5'
miRNA: 3'- -UGGGGcGG-CCGAAGUaa--------GCUUGGGUc -5'
miRNA: 3'- -UGGGGCGGCCGaaGUAaGCuUGGGuc -5'
miRNA: 3'- -UGGGGCGGCCGAAGUAAGCUUGGGUC- -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 | |||||||
| 12692 | 3' | -57.2 | NC_003347.1 | + | 1649 | 0.67 | 0.107839 |
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Target: 5'- gGCCUCGgCGGUgaccCAgUCGAACUCAGc -3' miRNA: 3'- -UGGGGCgGCCGaa--GUaAGCUUGGGUC- -5' |
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| 12692 | 3' | -57.2 | NC_003347.1 | + | 3132 | 0.69 | 0.083016 |
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Target: 5'- gACCCCcCCuGGCUUCAcucccaucacCGAGCCCAc -3' miRNA: 3'- -UGGGGcGG-CCGAAGUaa--------GCUUGGGUc -5' |
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| 12692 | 3' | -57.2 | NC_003347.1 | + | 5729 | 0.75 | 0.02399 |
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Target: 5'- gGCCCCGCCGGCgcCGUcCGcGCCCc- -3' miRNA: 3'- -UGGGGCGGCCGaaGUAaGCuUGGGuc -5' |
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| 12692 | 3' | -57.2 | NC_003347.1 | + | 1578 | 1.08 | 0.000041 |
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Target: 5'- gACCCCGCCGGCUUCAUUCGAACCCAGu -3' miRNA: 3'- -UGGGGCGGCCGAAGUAAGCUUGGGUC- -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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