miRNA: 3'- -GAGAGGGUCCGuuuau-GGUCU-----------UCGGC- -5'
miRNA: 3'- gaGAGGG------------UCCGUUUAUGG---UCuuCGGC- -5'
miRNA: 3'- gAGAGGGUCCgUUuaUGGUCuuCGGc -5'
miRNA: 3'- -GAGAGGGUCCGUUUAUGGUCUUCGGC- -5'
Results 21 - 24 of 24 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 | |||||||
| 2639 | 3' | -52.9 | NC_001491.2 | + | 32329 | 0.74 | 0.623174 |
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Target: 5'- gCUCUCCCGGGCcguccuCCGGAggggaucgcccGGCCGc -3' miRNA: 3'- -GAGAGGGUCCGuuuau-GGUCU-----------UCGGC- -5' |
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| 2639 | 3' | -52.9 | NC_001491.2 | + | 64659 | 0.75 | 0.612653 |
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Target: 5'- -gCUCCUgggucccugaggGGGCAGAUGCCgcuGGggGCCGc -3' miRNA: 3'- gaGAGGG------------UCCGUUUAUGG---UCuuCGGC- -5' |
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| 2639 | 3' | -52.9 | NC_001491.2 | + | 52826 | 0.79 | 0.379472 |
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Target: 5'- gUUUCCCAGGgGA--GCCAGggGCCa -3' miRNA: 3'- gAGAGGGUCCgUUuaUGGUCuuCGGc -5' |
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| 2639 | 3' | -52.9 | NC_001491.2 | + | 133309 | 1.1 | 0.004234 |
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Target: 5'- cCUCUCCCAGGCAAAUACCAGAAGCCGg -3' miRNA: 3'- -GAGAGGGUCCGUUUAUGGUCUUCGGC- -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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