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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 | |||||||
| 16400 | 3' | -54 | NC_004084.1 | + | 47265 | 0.66 | 0.790025 |
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Target: 5'- cUCGAGaaGCcGUCCCggucaGCAuccCAGUCGCc -3' miRNA: 3'- -AGCUCa-CGuCAGGGa----CGUu--GUCAGUG- -5' |
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| 16400 | 3' | -54 | NC_004084.1 | + | 49735 | 0.66 | 0.769786 |
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Target: 5'- cCGAGUccuCGGUCCaCUGCGuc-GUCACa -3' miRNA: 3'- aGCUCAc--GUCAGG-GACGUuguCAGUG- -5' |
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| 16400 | 3' | -54 | NC_004084.1 | + | 54606 | 0.66 | 0.759441 |
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Target: 5'- uUCGAGU-CAGUCaUCgGCGGC-GUCACg -3' miRNA: 3'- -AGCUCAcGUCAG-GGaCGUUGuCAGUG- -5' |
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| 16400 | 3' | -54 | NC_004084.1 | + | 41572 | 0.66 | 0.759441 |
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Target: 5'- cCGGGUGCGGUUCg-GCAucgGCGggcGUCGCg -3' miRNA: 3'- aGCUCACGUCAGGgaCGU---UGU---CAGUG- -5' |
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| 16400 | 3' | -54 | NC_004084.1 | + | 27326 | 0.66 | 0.748961 |
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Target: 5'- gUCGAGcGCGGUUCCggucugUGCAacuGCGGUCu- -3' miRNA: 3'- -AGCUCaCGUCAGGG------ACGU---UGUCAGug -5' |
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| 16400 | 3' | -54 | NC_004084.1 | + | 50600 | 0.68 | 0.661724 |
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Target: 5'- cUCGAG-GCAGUUCgUGCGuACGGguUCGCc -3' miRNA: 3'- -AGCUCaCGUCAGGgACGU-UGUC--AGUG- -5' |
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| 16400 | 3' | -54 | NC_004084.1 | + | 35480 | 0.69 | 0.572585 |
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Target: 5'- gUCGAG-GCGGcgaucgccgagaUCCCgacCAACGGUCGCg -3' miRNA: 3'- -AGCUCaCGUC------------AGGGac-GUUGUCAGUG- -5' |
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| 16400 | 3' | -54 | NC_004084.1 | + | 16274 | 1.09 | 0.001199 |
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Target: 5'- gUCGAGUGCAGUCCCUGCAACAGUCACc -3' miRNA: 3'- -AGCUCACGUCAGGGACGUUGUCAGUG- -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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