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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 | |||||||
| 2662 | 3' | -53.4 | NC_001491.2 | + | 123315 | 0.66 | 0.963343 |
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Target: 5'- --gGCgCgGGGcuccaucaagcGCGCUCCaGCGCGUGGa -3' miRNA: 3'- gaaCG-GaCUU-----------UGCGAGGaCGCGCAUC- -5' |
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| 2662 | 3' | -53.4 | NC_001491.2 | + | 14441 | 0.66 | 0.959769 |
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Target: 5'- gUUGCUUGGAACGCUCgUGUaaacCGUu- -3' miRNA: 3'- gAACGGACUUUGCGAGgACGc---GCAuc -5' |
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| 2662 | 3' | -53.4 | NC_001491.2 | + | 33127 | 0.66 | 0.951919 |
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Target: 5'- -cUGCCaGAAguucauccACGCUCC-GCGCGg-- -3' miRNA: 3'- gaACGGaCUU--------UGCGAGGaCGCGCauc -5' |
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| 2662 | 3' | -53.4 | NC_001491.2 | + | 72544 | 0.67 | 0.943102 |
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Target: 5'- --gGCCU--AGCGCUaaugGCGCGUGGg -3' miRNA: 3'- gaaCGGAcuUUGCGAgga-CGCGCAUC- -5' |
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| 2662 | 3' | -53.4 | NC_001491.2 | + | 42444 | 0.69 | 0.861657 |
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Target: 5'- uUUGCCUGGAcGCGCUuuucgCCccccgagaaggUGCGUGUAGu -3' miRNA: 3'- gAACGGACUU-UGCGA-----GG-----------ACGCGCAUC- -5' |
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| 2662 | 3' | -53.4 | NC_001491.2 | + | 91654 | 0.71 | 0.753511 |
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Target: 5'- -cUGCCUGAAacACGCgauuguuUCCUGCGCu--- -3' miRNA: 3'- gaACGGACUU--UGCG-------AGGACGCGcauc -5' |
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| 2662 | 3' | -53.4 | NC_001491.2 | + | 111546 | 0.72 | 0.744601 |
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Target: 5'- -gUGCCaaUGAGGCGUUUgUGCGCGUc- -3' miRNA: 3'- gaACGG--ACUUUGCGAGgACGCGCAuc -5' |
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| 2662 | 3' | -53.4 | NC_001491.2 | + | 87667 | 1.09 | 0.004787 |
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Target: 5'- aCUUGCCUGAAACGCUCCUGCGCGUAGc -3' miRNA: 3'- -GAACGGACUUUGCGAGGACGCGCAUC- -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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