miRNA: 3'- uCCGu---UCCGGCUCaAa-------------GGCUGCCGCC- -5'
miRNA: 3'- uCCGUUCCGGC-------UCAaAGGC------UGCCGCC- -5'
miRNA: 3'- uCCGUUC---------CGGCUCaaa-----GGCUGCCGCC- -5'
miRNA: 3'- -UCCGUUCCGGCUCAAAGGCUGCCGCC- -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 | |||||||
| 1420 | 5' | -57.4 | NC_001335.1 | + | 5853 | 0.72 | 0.29516 |
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Target: 5'- uGGCcagcGGGCCGAGcUgggggagagaaccgCUGACGGCGGu -3' miRNA: 3'- uCCGu---UCCGGCUCaAa-------------GGCUGCCGCC- -5' |
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| 1420 | 5' | -57.4 | NC_001335.1 | + | 24096 | 0.73 | 0.257385 |
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Target: 5'- cGGCGGGGCUGgugcccaGGUcUCCGcacagaGCGGCGGu -3' miRNA: 3'- uCCGUUCCGGC-------UCAaAGGC------UGCCGCC- -5' |
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| 1420 | 5' | -57.4 | NC_001335.1 | + | 2533 | 0.79 | 0.101203 |
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Target: 5'- cGGCAAGaaaucagccGCCGAGggcguagcCCGACGGCGGg -3' miRNA: 3'- uCCGUUC---------CGGCUCaaa-----GGCUGCCGCC- -5' |
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| 1420 | 5' | -57.4 | NC_001335.1 | + | 49813 | 1.1 | 0.000587 |
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Target: 5'- aAGGCAAGGCCGAGUUUCCGACGGCGGu -3' miRNA: 3'- -UCCGUUCCGGCUCAAAGGCUGCCGCC- -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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