miRNA: 3'- -UAGUAa---CGGAGGUuuCUUCUCUGcaa -5'
miRNA: 3'- -UAGUaaCGGaGGUU---UCUUCUCUGCAa -5'
miRNA: 3'- uaGUAa---CGGAGGU-------UUCUUCUCUGcaa -5'
miRNA: 3'- -UAGUAACGGAGGUUUCUUCUCUGCAA- -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 | |||||||
| 28342 | 5' | -48.8 | NC_005946.1 | + | 3028 | 0.68 | 0.964798 |
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Target: 5'- cGUCGUcccgGCCUCCA--GGAGGGACa-- -3' miRNA: 3'- -UAGUAa---CGGAGGUuuCUUCUCUGcaa -5' |
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| 28342 | 5' | -48.8 | NC_005946.1 | + | 16432 | 0.68 | 0.961046 |
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Target: 5'- cAUCAagGCCgCCGGagcAGAGGAGAUGUg -3' miRNA: 3'- -UAGUaaCGGaGGUU---UCUUCUCUGCAa -5' |
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| 28342 | 5' | -48.8 | NC_005946.1 | + | 28744 | 0.68 | 0.960657 |
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Target: 5'- -cCAUggugGCCUCCAucaccuuGGGAGGAGGCa-- -3' miRNA: 3'- uaGUAa---CGGAGGU-------UUCUUCUCUGcaa -5' |
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| 28342 | 5' | -48.8 | NC_005946.1 | + | 8634 | 1.04 | 0.01443 |
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Target: 5'- cAUCAUUGCCUCCAAAGAAGAGACGUUg -3' miRNA: 3'- -UAGUAACGGAGGUUUCUUCUCUGCAA- -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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