miRNA: 3'- -UUGCAGGagaaagGUCCACAGAGGUu -5'
miRNA: 3'- uuGCAGGAGaaaGGUCCAC--AGAGGUu -5'
miRNA: 3'- uugCAGGAGAAAGGUCC-----ACAGAGGuu -5'
miRNA: 3'- -UUGCAG-----------GAGaAAGGUCCACAGAGGUU- -5'
miRNA: 3'- -UUGCAGGAGAAAGGUCCACAGAGGUU- -5'
Results 1 - 5 of 5 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 | |||||||
| 14367 | 5' | -53.4 | NC_003521.1 | + | 120472 | 0.7 | 0.878437 |
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Target: 5'- cGACGUCCg-----CAGGUGUCUCCGc -3' miRNA: 3'- -UUGCAGGagaaagGUCCACAGAGGUu -5' |
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| 14367 | 5' | -53.4 | NC_003521.1 | + | 168697 | 0.72 | 0.81429 |
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Target: 5'- -cCGUCCUCgg-UCAGGUGaaUCUCCAc -3' miRNA: 3'- uuGCAGGAGaaaGGUCCAC--AGAGGUu -5' |
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| 14367 | 5' | -53.4 | NC_003521.1 | + | 71603 | 0.73 | 0.749251 |
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Target: 5'- --gGUCCUCUUUCUGGGauuguUGUCUCCu- -3' miRNA: 3'- uugCAGGAGAAAGGUCC-----ACAGAGGuu -5' |
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| 14367 | 5' | -53.4 | NC_003521.1 | + | 193527 | 0.74 | 0.71962 |
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Target: 5'- gGACGUUcgcucggcacgCUCcUUCCAGGUGUCUUCAAc -3' miRNA: 3'- -UUGCAG-----------GAGaAAGGUCCACAGAGGUU- -5' |
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| 14367 | 5' | -53.4 | NC_003521.1 | + | 47314 | 1.04 | 0.014166 |
|
Target: 5'- gAACGUCCUCUUUCCAGGUGUCUCCAAc -3' miRNA: 3'- -UUGCAGGAGAAAGGUCCACAGAGGUU- -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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