miRNA: 3'- caagCGU-UUUGa-----GGGCCGU--UCUCUAG- -5'
miRNA: 3'- caaGCGUU------------UugAGGGCCGUU---------------CUCUAG- -5'
miRNA: 3'- caaGCGUuuUGAGGGCCGU----UCuCUAG- -5'
Results 1 - 3 of 3 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 | |||||||
| 7581 | 3' | -50 | NC_001962.1 | + | 48013 | 0.66 | 0.993027 |
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Target: 5'- ---gGCAcGGAUuuugugCCCGGCAacGGAGAUCg -3' miRNA: 3'- caagCGU-UUUGa-----GGGCCGU--UCUCUAG- -5' |
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| 7581 | 3' | -50 | NC_001962.1 | + | 41247 | 0.67 | 0.988479 |
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Target: 5'- --aCGCGGcgggcacaugacAugUCCCGGCGGgaugccgccguaauuGAGAUCg -3' miRNA: 3'- caaGCGUU------------UugAGGGCCGUU---------------CUCUAG- -5' |
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| 7581 | 3' | -50 | NC_001962.1 | + | 98687 | 0.7 | 0.940932 |
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Target: 5'- --aCGCG--AUUCCCGGCAcgccGGuGAUCg -3' miRNA: 3'- caaGCGUuuUGAGGGCCGU----UCuCUAG- -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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