miRNA: 3'- -ACGGCaaCAG-CACCUCCAaac--GGCUG- -5'
miRNA: 3'- aCGGCaaCAGCa----CCUCCaaaCGGCUG- -5'
miRNA: 3'- -ACGGCaa----CAgCACCuCCAaaCGGCUG- -5'
miRNA: 3'- aCGGCAACaGCA------CCUCCaa-ACG-GCUG- -5'
Results 1 - 4 of 4 are showing below:
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| ID | Location | Perfect MFE.* | RefSeq Acc. |
strand
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Start Position | R_P_ratio# | P value |
| Predicted miRNA align pattern | |||||||
| 22180 | 3' | -54.5 | NC_004927.1 | + | 4615 | 0.73 | 0.426745 |
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Target: 5'- cUGCCGgaGUCgGUGGAGGUaaucuCCGACc -3' miRNA: 3'- -ACGGCaaCAG-CACCUCCAaac--GGCUG- -5' |
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| 22180 | 3' | -54.5 | NC_004927.1 | + | 75542 | 0.71 | 0.558108 |
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Target: 5'- aGUCGggGUCGgauggGGAGGg--GUCGGCu -3' miRNA: 3'- aCGGCaaCAGCa----CCUCCaaaCGGCUG- -5' |
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| 22180 | 3' | -54.5 | NC_004927.1 | + | 50395 | 0.67 | 0.770951 |
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Target: 5'- cUGCCGggagcgGUgGUGGuGGU--GCUGGCg -3' miRNA: 3'- -ACGGCaa----CAgCACCuCCAaaCGGCUG- -5' |
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| 22180 | 3' | -54.5 | NC_004927.1 | + | 68015 | 0.66 | 0.836688 |
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Target: 5'- cGCUGUUGgCGUccugauGGAGGacgUGCgCGACc -3' miRNA: 3'- aCGGCAACaGCA------CCUCCaa-ACG-GCUG- -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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