miRNA: 3'- guuGUCGUUCCGGUa-----AGCGG---CC-CGGU- -5'
miRNA: 3'- guUGUcGUUCCGGuaAGCGGCCCGGu -5'
miRNA: 3'- -GUUGUCGu----UCCGGua--AGCGGCCCGGu -5'
miRNA: 3'- -GUUGUCGUUCCGGUAAGCGGCCCGGU- -5'
Results 21 - 24 of 24 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 | |||||||
| 12472 | 3' | -57.4 | NC_003324.1 | + | 51719 | 0.69 | 0.37858 |
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Target: 5'- --uCAGCGAGGCCGacgcaaUCGCCgagGGcGCCAa -3' miRNA: 3'- guuGUCGUUCCGGUa-----AGCGG---CC-CGGU- -5' |
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| 12472 | 3' | -57.4 | NC_003324.1 | + | 53816 | 0.7 | 0.361226 |
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Target: 5'- -uGCAcCAAGGUC--UCGCCGGGCUg -3' miRNA: 3'- guUGUcGUUCCGGuaAGCGGCCCGGu -5' |
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| 12472 | 3' | -57.4 | NC_003324.1 | + | 29243 | 0.77 | 0.123645 |
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Target: 5'- aCGGCGGCuguucGGGCCugcaUCGCCGGGCUc -3' miRNA: 3'- -GUUGUCGu----UCCGGua--AGCGGCCCGGu -5' |
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| 12472 | 3' | -57.4 | NC_003324.1 | + | 42657 | 1.08 | 0.000694 |
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Target: 5'- gCAACAGCAAGGCCAUUCGCCGGGCCAc -3' miRNA: 3'- -GUUGUCGUUCCGGUAAGCGGCCCGGU- -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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