miRNA: 3'- -GCCGaAGC--UCa-GGA---UGCUCCGGCUGC- -5'
miRNA: 3'- -GCCGAAGCUCAg--GAUGcUCC---------GGCUGC- -5'
miRNA: 3'- gCCgaa----GCUCAGGa---------UGCUCCGGCUGC- -5'
miRNA: 3'- -GCCGAAGCUCaGGauGCUCCgGCUGC- -5'
miRNA: 3'- -GCCGAAGCUCAGGAUGCUCCGGCUGC- -5'
Results 21 - 25 of 25 are showing below:
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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 | |||||||
| 16448 | 5' | -57 | NC_004084.1 | + | 47259 | 0.7 | 0.420724 |
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Target: 5'- cCGGC-UCGccGGcgCCUacuACGAGGUCGACGa -3' miRNA: 3'- -GCCGaAGC--UCa-GGA---UGCUCCGGCUGC- -5' |
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| 16448 | 5' | -57 | NC_004084.1 | + | 2997 | 0.7 | 0.411577 |
|
Target: 5'- uCGGCUUCGGGUagaCUACcGGGacagcguccCCGACGu -3' miRNA: 3'- -GCCGAAGCUCAg--GAUGcUCC---------GGCUGC- -5' |
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| 16448 | 5' | -57 | NC_004084.1 | + | 41817 | 0.71 | 0.384888 |
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Target: 5'- aGGagcccgcCGGGUCCguagggggugACGAGGCCGAUGg -3' miRNA: 3'- gCCgaa----GCUCAGGa---------UGCUCCGGCUGC- -5' |
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| 16448 | 5' | -57 | NC_004084.1 | + | 56915 | 0.74 | 0.26286 |
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Target: 5'- uCGGCUUCGAG-CU--CGAGGgCGACGu -3' miRNA: 3'- -GCCGAAGCUCaGGauGCUCCgGCUGC- -5' |
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| 16448 | 5' | -57 | NC_004084.1 | + | 40111 | 1.1 | 0.000802 |
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Target: 5'- gCGGCUUCGAGUCCUACGAGGCCGACGg -3' miRNA: 3'- -GCCGAAGCUCAGGAUGCUCCGGCUGC- -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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