miRNA: 3'- aagCGGGCAUu----GCAGG------UGCUCCAGUu -5'
miRNA: 3'- aAGCGGGCAUugCaGGuGCUCCaguu -5'
miRNA: 3'- aaGCGGGCAuuGCAGGuGCUCCAGUU- -5'
miRNA: 3'- aAGCGGgCaUUGCa-----GGUGC-UCCAGUU- -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 | |||||||
| 22173 | 5' | -55.7 | NC_004927.1 | + | 11123 | 0.66 | 0.715954 |
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Target: 5'- --aGUCCGUGucccuCGUCCacaaucACGAGGUCGc -3' miRNA: 3'- aagCGGGCAUu----GCAGG------UGCUCCAGUu -5' |
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| 22173 | 5' | -55.7 | NC_004927.1 | + | 24120 | 0.67 | 0.705348 |
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Target: 5'- gUCGUCCGUGugGcCC-CGAGGg--- -3' miRNA: 3'- aAGCGGGCAUugCaGGuGCUCCaguu -5' |
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| 22173 | 5' | -55.7 | NC_004927.1 | + | 43035 | 0.7 | 0.512154 |
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Target: 5'- -cUGCCCGU--CGUUCcCGAGGUCGAu -3' miRNA: 3'- aaGCGGGCAuuGCAGGuGCUCCAGUU- -5' |
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| 22173 | 5' | -55.7 | NC_004927.1 | + | 20234 | 0.7 | 0.481516 |
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Target: 5'- cUCGCCgGgGACGgacuugCCACGgAGGUCGAa -3' miRNA: 3'- aAGCGGgCaUUGCa-----GGUGC-UCCAGUU- -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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