miRNA: 3'- -CGGc---GGGUAG---UGCGGU--GGGUUCCGuu -5'
miRNA: 3'- -CggCGGg------UAGUGCGGU--GGGuUCCGUU- -5'
miRNA: 3'- cGGCGGGUAGugCGG------------UgGGUUCCGuu -5'
miRNA: 3'- -CgGCGGGUAGUGCGGUGGGUUCCGUU- -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 | |||||||
| 8278 | 3' | -59.9 | NC_002031.1 | + | 9667 | 0.66 | 0.124229 |
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Target: 5'- gGCCcuguCCCAUCucaACGCCAugUCCAAGGUu- -3' miRNA: 3'- -CGGc---GGGUAG---UGCGGU--GGGUUCCGuu -5' |
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| 8278 | 3' | -59.9 | NC_002031.1 | + | 3330 | 0.66 | 0.120418 |
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Target: 5'- aGuuGCCaucaaugAUCACGCUAguCCCuGGGCAAg -3' miRNA: 3'- -CggCGGg------UAGUGCGGU--GGGuUCCGUU- -5' |
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| 8278 | 3' | -59.9 | NC_002031.1 | + | 6199 | 0.66 | 0.113121 |
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Target: 5'- cCUGCCCGUUugGCUuucguggcaaguGgCCAAGGCu- -3' miRNA: 3'- cGGCGGGUAGugCGG------------UgGGUUCCGuu -5' |
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| 8278 | 3' | -59.9 | NC_002031.1 | + | 3879 | 0.99 | 0.000171 |
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Target: 5'- aGgCGCCCAUCACGCCACCCAAGGCAAu -3' miRNA: 3'- -CgGCGGGUAGUGCGGUGGGUUCCGUU- -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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