miRNA: 3'- cUUGGAg--GCUCUGCGc---CGGGAGUUcu -5'
miRNA: 3'- -CUUGGaGGCUCugCG---CCGGGaGUU-CU- -5'
miRNA: 3'- -CUUGGAGGCUC------------UGCGCc--GGGAGUUcu -5'
miRNA: 3'- -CUUGGAGGcuc-UGCGCCG---GGAGUUCU- -5'
miRNA: 3'- cuUGGAGGcuCUGCGCCG---GGAGUUCU- -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 | |||||||
| 22183 | 3' | -57.3 | NC_004927.1 | + | 58404 | 0.66 | 0.669458 |
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Target: 5'- aGACCUguaCGAGACGUuccaGCCCUCGAu- -3' miRNA: 3'- cUUGGAg--GCUCUGCGc---CGGGAGUUcu -5' |
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| 22183 | 3' | -57.3 | NC_004927.1 | + | 70647 | 0.67 | 0.637634 |
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Target: 5'- gGAGCCgCCGGGugGUgguGGCCC-CGAcGAc -3' miRNA: 3'- -CUUGGaGGCUCugCG---CCGGGaGUU-CU- -5' |
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| 22183 | 3' | -57.3 | NC_004927.1 | + | 58642 | 0.67 | 0.627004 |
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Target: 5'- cGAACCUUCGAGgcauuauccguaGCGCGauuCCCUCGAu- -3' miRNA: 3'- -CUUGGAGGCUC------------UGCGCc--GGGAGUUcu -5' |
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| 22183 | 3' | -57.3 | NC_004927.1 | + | 45965 | 0.67 | 0.616379 |
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Target: 5'- uGAGCCUCCuacaACGUGGCgaaCUUCAAGAa -3' miRNA: 3'- -CUUGGAGGcuc-UGCGCCG---GGAGUUCU- -5' |
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| 22183 | 3' | -57.3 | NC_004927.1 | + | 56669 | 0.67 | 0.605767 |
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Target: 5'- -uACCUCCccGACGCGGUucaCUUCGGGGc -3' miRNA: 3'- cuUGGAGGcuCUGCGCCG---GGAGUUCU- -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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