miRNA: 3'- -UUGCGUuuaa-------GCCCGC-GCuUAGGCAa -5'
miRNA: 3'- uugCGUUUaa--GCCCGCGCuUAGGCaa -5'
miRNA: 3'- -UUGCgUUUAagCCCG-------CGCUUAGGCAa -5'
miRNA: 3'- uUGCGUUuaaGCCCGCGc--UUAGGCAa -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 | |||||||
| 30664 | 5' | -52.2 | NC_006549.1 | + | 91310 | 0.66 | 0.972968 |
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Target: 5'- aGGCGCAuugacuugcgaCGGGCGuCGcGUCCGUg -3' miRNA: 3'- -UUGCGUuuaa-------GCCCGC-GCuUAGGCAa -5' |
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| 30664 | 5' | -52.2 | NC_006549.1 | + | 116954 | 0.68 | 0.924905 |
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Target: 5'- --aGCAGAgcggCGGGCGCGuAUCUGc- -3' miRNA: 3'- uugCGUUUaa--GCCCGCGCuUAGGCaa -5' |
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| 30664 | 5' | -52.2 | NC_006549.1 | + | 74542 | 0.69 | 0.899448 |
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Target: 5'- uGACGgAAAUagGGGCcguguggGCGGAUCCGUc -3' miRNA: 3'- -UUGCgUUUAagCCCG-------CGCUUAGGCAa -5' |
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| 30664 | 5' | -52.2 | NC_006549.1 | + | 91525 | 0.75 | 0.563821 |
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Target: 5'- cGCGCAAug-CGGGCGCaccGAUCCGUa -3' miRNA: 3'- uUGCGUUuaaGCCCGCGc--UUAGGCAa -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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