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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 | |||||||
| 28133 | 5' | -55 | NC_005887.1 | + | 929 | 0.7 | 0.428429 |
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Target: 5'- cGGCGCGGGccACGcg-UCCAcGGGCaCCu -3' miRNA: 3'- -CCGCGCCCu-UGCuaaAGGU-CUCGcGG- -5' |
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| 28133 | 5' | -55 | NC_005887.1 | + | 34651 | 0.7 | 0.418822 |
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Target: 5'- aGGCGCGccGGcuugcCGGUUUCCGGAucCGCCa -3' miRNA: 3'- -CCGCGC--CCuu---GCUAAAGGUCUc-GCGG- -5' |
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| 28133 | 5' | -55 | NC_005887.1 | + | 35939 | 0.71 | 0.409346 |
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Target: 5'- gGGCGCGGcGucGCGGUgucugCC-GAGCGCa -3' miRNA: 3'- -CCGCGCC-Cu-UGCUAaa---GGuCUCGCGg -5' |
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| 28133 | 5' | -55 | NC_005887.1 | + | 35383 | 0.71 | 0.38989 |
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Target: 5'- cGGCGCGcggcaguGGAGCGAUg--CAGAGaagGCCg -3' miRNA: 3'- -CCGCGC-------CCUUGCUAaagGUCUCg--CGG- -5' |
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| 28133 | 5' | -55 | NC_005887.1 | + | 23345 | 0.71 | 0.381738 |
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Target: 5'- cGGCGCGGGcuGCGGcaaccgCCAcGAgcuGCGCCu -3' miRNA: 3'- -CCGCGCCCu-UGCUaaa---GGU-CU---CGCGG- -5' |
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| 28133 | 5' | -55 | NC_005887.1 | + | 15930 | 0.72 | 0.355399 |
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Target: 5'- cGCGCGGGccggaauCGAUgcgCCGGccacGCGCCg -3' miRNA: 3'- cCGCGCCCuu-----GCUAaa-GGUCu---CGCGG- -5' |
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| 28133 | 5' | -55 | NC_005887.1 | + | 37445 | 0.72 | 0.355399 |
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Target: 5'- aGCGCGGcGcuugccugcGCGGUUUgCAGuGCGCCg -3' miRNA: 3'- cCGCGCCcU---------UGCUAAAgGUCuCGCGG- -5' |
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| 28133 | 5' | -55 | NC_005887.1 | + | 17651 | 0.72 | 0.346909 |
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Target: 5'- aGCGCGGGAuugACGGgcgugUUCGucGCGCCg -3' miRNA: 3'- cCGCGCCCU---UGCUaa---AGGUcuCGCGG- -5' |
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| 28133 | 5' | -55 | NC_005887.1 | + | 11374 | 0.78 | 0.1494 |
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Target: 5'- aGCGCGGGcgucAGCGcag-CCGGAGCGCUg -3' miRNA: 3'- cCGCGCCC----UUGCuaaaGGUCUCGCGG- -5' |
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| 28133 | 5' | -55 | NC_005887.1 | + | 13759 | 1.01 | 0.003362 |
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Target: 5'- uGGCGCGaGGACGAUUUCCAGAGCGCCg -3' miRNA: 3'- -CCGCGCcCUUGCUAAAGGUCUCGCGG- -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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