miRNA: 3'- -UCCGGCCCUUUa---------UGg--GUCGG-AgCGAa -5'
miRNA: 3'- uCCGGC-CCUUUauGGGUCGGa---GCGAA- -5'
miRNA: 3'- -UCCGGCCCuuuauGGGUCGGAGcGAa -5'
miRNA: 3'- -UCCGGCCCUUUAUGGGUCGGAGCGAA- -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 | |||||||
| 21945 | 3' | -58.2 | NC_004913.1 | + | 9666 | 0.66 | 0.507289 |
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Target: 5'- gGGGCCGGGAAAcauuauugagACaaaCAGCCaUgGCUg -3' miRNA: 3'- -UCCGGCCCUUUa---------UGg--GUCGG-AgCGAa -5' |
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| 21945 | 3' | -58.2 | NC_004913.1 | + | 59661 | 0.69 | 0.364472 |
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Target: 5'- uGGCUGuGGAAAauCCCAGCUggcgCGCUUu -3' miRNA: 3'- uCCGGC-CCUUUauGGGUCGGa---GCGAA- -5' |
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| 21945 | 3' | -58.2 | NC_004913.1 | + | 37677 | 0.69 | 0.364472 |
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Target: 5'- gAGGCUGGGuauuuCCCGGCCUUuCUg -3' miRNA: 3'- -UCCGGCCCuuuauGGGUCGGAGcGAa -5' |
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| 21945 | 3' | -58.2 | NC_004913.1 | + | 37596 | 1.04 | 0.000967 |
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Target: 5'- aAGGCCGGGAAAUACCCAGCCUCGCUUu -3' miRNA: 3'- -UCCGGCCCUUUAUGGGUCGGAGCGAA- -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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