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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 | |||||||
| 28378 | 5' | -54.4 | NC_005946.1 | + | 62132 | 0.66 | 0.859768 |
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Target: 5'- -cGCUCAcgGCgcagccagGGAGAGgggcuCCGUCUCUCu -3' miRNA: 3'- caCGAGUa-CGa-------CCUCUU-----GGUAGGGAG- -5' |
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| 28378 | 5' | -54.4 | NC_005946.1 | + | 99140 | 0.68 | 0.748969 |
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Target: 5'- aUGCUCAgcuucuUGUUGGugcAGAACCAccacugCCCUCc -3' miRNA: 3'- cACGAGU------ACGACC---UCUUGGUa-----GGGAG- -5' |
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| 28378 | 5' | -54.4 | NC_005946.1 | + | 66107 | 0.7 | 0.654179 |
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Target: 5'- -aGCUCAUGCacaugUGGAGGuCCAUgCCCg- -3' miRNA: 3'- caCGAGUACG-----ACCUCUuGGUA-GGGag -5' |
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| 28378 | 5' | -54.4 | NC_005946.1 | + | 67565 | 0.71 | 0.600343 |
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Target: 5'- -gGCUgGUgaGCUGGAGGACCGgcugggCCCUg -3' miRNA: 3'- caCGAgUA--CGACCUCUUGGUa-----GGGAg -5' |
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| 28378 | 5' | -54.4 | NC_005946.1 | + | 25363 | 0.71 | 0.57893 |
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Target: 5'- cGUGUUUAUGCUGGGGAAgC-UCCUg- -3' miRNA: 3'- -CACGAGUACGACCUCUUgGuAGGGag -5' |
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| 28378 | 5' | -54.4 | NC_005946.1 | + | 94915 | 0.72 | 0.56722 |
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Target: 5'- -gGCUUuuAUGCggaGGAGAGCCccggacuGUCCCUCu -3' miRNA: 3'- caCGAG--UACGa--CCUCUUGG-------UAGGGAG- -5' |
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| 28378 | 5' | -54.4 | NC_005946.1 | + | 98026 | 0.72 | 0.527298 |
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Target: 5'- gGUGUU-GUGCUGGAGGAUCAggaggucguggauggCCCUCa -3' miRNA: 3'- -CACGAgUACGACCUCUUGGUa--------------GGGAG- -5' |
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| 28378 | 5' | -54.4 | NC_005946.1 | + | 41102 | 1.09 | 0.00213 |
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Target: 5'- gGUGCUCAUGCUGGAGAACCAUCCCUCu -3' miRNA: 3'- -CACGAGUACGACCUCUUGGUAGGGAG- -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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