miRNA: 3'- -GCUGCU-----UGCGCa---UGUC---CCGGUGG-GCa -5'
miRNA: 3'- gCUGCUUGCGCAugUCcCGGUG-------GGCa -5'
miRNA: 3'- gcUGCUUGCGC--AUGUCCCGGUGgGCa -5'
miRNA: 3'- gCUGcu--UGCGCa---UGUCCCGGUGG-GCa -5'
miRNA: 3'- -GCUGCUUGCGCa--UGUCcCGGUgGGca -5'
Results 21 - 25 of 25 are showing below:
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| ID | Location | Perfect MFE.* | RefSeq Acc. |
strand
|
Start Position | R_P_ratio# | P value |
| Predicted miRNA align pattern | |||||||
| 23214 | 3' | -58 | NC_005259.1 | + | 26515 | 0.69 | 0.454486 |
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Target: 5'- cCGGCGAgaagaGCGCGgugaGCAGcuuGGCCACCaCGa -3' miRNA: 3'- -GCUGCU-----UGCGCa---UGUC---CCGGUGG-GCa -5' |
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| 23214 | 3' | -58 | NC_005259.1 | + | 44317 | 0.69 | 0.463063 |
|
Target: 5'- uGACGAGCGUGUugAGcGCCGCguagcugCCGg -3' miRNA: 3'- gCUGCUUGCGCAugUCcCGGUG-------GGCa -5' |
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| 23214 | 3' | -58 | NC_005259.1 | + | 33105 | 0.69 | 0.473661 |
|
Target: 5'- -cGCGAGCGUGccUGUAGGGCCACgCGg -3' miRNA: 3'- gcUGCUUGCGC--AUGUCCCGGUGgGCa -5' |
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| 23214 | 3' | -58 | NC_005259.1 | + | 8666 | 0.69 | 0.483399 |
|
Target: 5'- gGGCugccACGCGggcaACGGGGCCGCCuCGa -3' miRNA: 3'- gCUGcu--UGCGCa---UGUCCCGGUGG-GCa -5' |
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| 23214 | 3' | -58 | NC_005259.1 | + | 58933 | 0.66 | 0.679881 |
|
Target: 5'- uCGGCGGGCGCGgugGCAGcGUCGgCCu- -3' miRNA: 3'- -GCUGCUUGCGCa--UGUCcCGGUgGGca -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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