miRNA: 3'- -UGGUgCCGGUagUACU-CGA-------ACGCGGC- -5'
miRNA: 3'- -UGGUGCCGGUAG---------------UACU--CGAa---CGCGGC- -5'
miRNA: 3'- -UGGUGCCG---------GUAGUACUCGaaCGCGGc -5'
miRNA: 3'- -UGGUGCCGGUAGUACUCGAACGCGGC- -5'
Results 1 - 4 of 4 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 | |||||||
| 323 | 5' | -57.2 | AC_000010.1 | + | 22570 | 0.66 | 0.448621 |
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Target: 5'- gACCA-GGCCAagAUGAuGCUaucccucUGCGCUGc -3' miRNA: 3'- -UGGUgCCGGUagUACU-CGA-------ACGCGGC- -5' |
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| 323 | 5' | -57.2 | AC_000010.1 | + | 8008 | 0.68 | 0.350174 |
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Target: 5'- uACUGCGGCCGUCuguacaagcacaagcAUGAauGCUcggcGCGCCGc -3' miRNA: 3'- -UGGUGCCGGUAG---------------UACU--CGAa---CGCGGC- -5' |
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| 323 | 5' | -57.2 | AC_000010.1 | + | 18715 | 0.73 | 0.160152 |
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Target: 5'- gACUGCGGUcgguggucaCAUCAUGGGUggGCGCCa -3' miRNA: 3'- -UGGUGCCG---------GUAGUACUCGaaCGCGGc -5' |
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| 323 | 5' | -57.2 | AC_000010.1 | + | 24807 | 1.07 | 0.000421 |
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Target: 5'- cACCACGGCCAUCAUGAGCUUGCGCCGc -3' miRNA: 3'- -UGGUGCCGGUAGUACUCGAACGCGGC- -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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