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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 | |||||||
| 13350 | 3' | -46.8 | NC_003409.1 | + | 62289 | 0.66 | 0.999865 |
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Target: 5'- gGCAUACugGGAUCCCUucaCAGuGCGaUAGGg -3' miRNA: 3'- -UGUAUG--UCUAGGGA---GUCuUGUgAUUC- -5' |
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| 13350 | 3' | -46.8 | NC_003409.1 | + | 59119 | 0.66 | 0.999865 |
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Target: 5'- gGCGUACAGAgUCCC-CAGu-CGCUc-- -3' miRNA: 3'- -UGUAUGUCU-AGGGaGUCuuGUGAuuc -5' |
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| 13350 | 3' | -46.8 | NC_003409.1 | + | 22017 | 0.66 | 0.999824 |
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Target: 5'- gACGguUACAGGUCCCUCccGAGcCACg--- -3' miRNA: 3'- -UGU--AUGUCUAGGGAGu-CUU-GUGauuc -5' |
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| 13350 | 3' | -46.8 | NC_003409.1 | + | 67193 | 0.67 | 0.999531 |
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Target: 5'- cCGUACcccUCUCUUAGGACACUGAu -3' miRNA: 3'- uGUAUGucuAGGGAGUCUUGUGAUUc -5' |
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| 13350 | 3' | -46.8 | NC_003409.1 | + | 74489 | 0.68 | 0.99758 |
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Target: 5'- -gGUACAG-UCCUUgCAGAAUACUGGa -3' miRNA: 3'- ugUAUGUCuAGGGA-GUCUUGUGAUUc -5' |
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| 13350 | 3' | -46.8 | NC_003409.1 | + | 80399 | 0.69 | 0.994385 |
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Target: 5'- ----cCAGcUCCCUUAGAGCACUugAAGa -3' miRNA: 3'- uguauGUCuAGGGAGUCUUGUGA--UUC- -5' |
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| 13350 | 3' | -46.8 | NC_003409.1 | + | 98692 | 0.7 | 0.98975 |
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Target: 5'- -gGUACGGGUaCCUCgaugcugAGAGCGCUGAGu -3' miRNA: 3'- ugUAUGUCUAgGGAG-------UCUUGUGAUUC- -5' |
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| 13350 | 3' | -46.8 | NC_003409.1 | + | 130970 | 1.1 | 0.015874 |
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Target: 5'- aACAUACAGAUCCCUCAGAACACUAAGa -3' miRNA: 3'- -UGUAUGUCUAGGGAGUCUUGUGAUUC- -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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