miRNA: 3'- cGUCGCaCUGGUaGCACUGGU------AGCGC- -5'
miRNA: 3'- -CGUCGcacUGGUa--GCACUGGUAGCGc -5'
miRNA: 3'- -CGUCGCACUGGUa---GCaCUgGUAGCgc -5'
miRNA: 3'- cgUCGCaCUGGU---AGCA----CUGG--UAGCGC- -5'
miRNA: 3'- -CGUCGCa---CUGg----UAGCa--CUGGuAGCGC- -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 | |||||||
| 23514 | 3' | -54.3 | NC_005259.1 | + | 46292 | 0.7 | 0.631569 |
|
Target: 5'- aCAGCGgGGCCGcCGUGGCUGcguuguUCGCGg -3' miRNA: 3'- cGUCGCaCUGGUaGCACUGGU------AGCGC- -5' |
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| 23514 | 3' | -54.3 | NC_005259.1 | + | 58465 | 0.69 | 0.685522 |
|
Target: 5'- cGCGGCc--ACCAgugCGUGGCUGUCGCc -3' miRNA: 3'- -CGUCGcacUGGUa--GCACUGGUAGCGc -5' |
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| 23514 | 3' | -54.3 | NC_005259.1 | + | 67980 | 0.69 | 0.696205 |
|
Target: 5'- aGCGGCGUGGCCAccgcCGcGAgCGUCGa- -3' miRNA: 3'- -CGUCGCACUGGUa---GCaCUgGUAGCgc -5' |
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| 23514 | 3' | -54.3 | NC_005259.1 | + | 4318 | 0.68 | 0.727852 |
|
Target: 5'- -gAGCGcGACCAaccUCGUgccgGACCucGUCGCGg -3' miRNA: 3'- cgUCGCaCUGGU---AGCA----CUGG--UAGCGC- -5' |
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| 23514 | 3' | -54.3 | NC_005259.1 | + | 47793 | 0.66 | 0.851648 |
|
Target: 5'- cGCAGCGguccGACggugaGUCGcgaGACC-UCGCGg -3' miRNA: 3'- -CGUCGCa---CUGg----UAGCa--CUGGuAGCGC- -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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