miRNA: 3'- -UGCAaaAGUGGU-GGAGG----------AGcGUGGCG- -5'
miRNA: 3'- -UGCAaaaGUGGUGGAGGa--GCG----UGGCG- -5'
miRNA: 3'- -UGCaaaa-GUGGUGGaGGAGcGUGGCG- -5'
miRNA: 3'- uGCAAAAGU----GGUGGAGGaGCGUGGCG- -5'
miRNA: 3'- -UGCaaa--AGUGGUGG--AGGAgCGUgGCG- -5'
Results 21 - 25 of 25 are showing below:
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| ID | Location | Perfect MFE.* | RefSeq Acc. | strand |
Start Position
|
R_P_ratio# | P value |
| Predicted miRNA align pattern | |||||||
| 13309 | 3' | -53.7 | NC_003409.1 | + | 107239 | 0.69 | 0.862047 |
|
Target: 5'- aACGUg-UCGCCAcCCUCCugcaacaggcUCcCACCGCg -3' miRNA: 3'- -UGCAaaAGUGGU-GGAGG----------AGcGUGGCG- -5' |
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| 13309 | 3' | -53.7 | NC_003409.1 | + | 109615 | 0.7 | 0.829451 |
|
Target: 5'- uGCGUg--CGCCGCCUCCgcgUGCgaagGCUGUu -3' miRNA: 3'- -UGCAaaaGUGGUGGAGGa--GCG----UGGCG- -5' |
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| 13309 | 3' | -53.7 | NC_003409.1 | + | 110014 | 0.74 | 0.602366 |
|
Target: 5'- uGCGccgggCGCCACCgCCUCcCGCCGCg -3' miRNA: 3'- -UGCaaaa-GUGGUGGaGGAGcGUGGCG- -5' |
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| 13309 | 3' | -53.7 | NC_003409.1 | + | 131423 | 0.82 | 0.250873 |
|
Target: 5'- cUGUUUUCGugccCCACCUCCcCGCGCCGUg -3' miRNA: 3'- uGCAAAAGU----GGUGGAGGaGCGUGGCG- -5' |
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| 13309 | 3' | -53.7 | NC_003409.1 | + | 133478 | 0.66 | 0.955666 |
|
Target: 5'- uGCGcaccaUCGCCACCacUCCUgGCAaCGCc -3' miRNA: 3'- -UGCaaa--AGUGGUGG--AGGAgCGUgGCG- -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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