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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 | |||||||
| 2517 | 3' | -57 | NC_001454.1 | + | 31843 | 0.66 | 0.451918 |
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Target: 5'- aGUCAAGCUCUCcacggGUUCUCgccucuguuguAGUCUGCCAa -3' miRNA: 3'- -CGGUUUGGGGG-----CAAGGG-----------UCAGACGGU- -5' |
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| 2517 | 3' | -57 | NC_001454.1 | + | 11380 | 0.68 | 0.340389 |
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Target: 5'- cGCCAAcauaaccagccGCCUCCaGggCCCGGgcgcugggCUGCCAu -3' miRNA: 3'- -CGGUU-----------UGGGGG-CaaGGGUCa-------GACGGU- -5' |
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| 2517 | 3' | -57 | NC_001454.1 | + | 23762 | 0.69 | 0.307913 |
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Target: 5'- uGCCAGACUCCCauag-CGGUUUGCCAg -3' miRNA: 3'- -CGGUUUGGGGGcaaggGUCAGACGGU- -5' |
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| 2517 | 3' | -57 | NC_001454.1 | + | 5133 | 0.7 | 0.27072 |
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Target: 5'- cGCCcuaaaauGCCUCCGcugUCCCAG-CUGUCAg -3' miRNA: 3'- -CGGuu-----UGGGGGCa--AGGGUCaGACGGU- -5' |
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| 2517 | 3' | -57 | NC_001454.1 | + | 12764 | 1.1 | 0.000298 |
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Target: 5'- gGCCAAACCCCCGUUCCCAGUCUGCCAu -3' miRNA: 3'- -CGGUUUGGGGGCAAGGGUCAGACGGU- -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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