miRNA: 3'- cCCGGGGGUCU---------------GGUAUU--GACGG---ACCU- -5'
miRNA: 3'- -CCCGgGGG----UCUGGUa--UUGACGG-----ACCU- -5'
miRNA: 3'- ccCGGGGGUCUGGuauuGACGGACCU- -5'
miRNA: 3'- -CCCGGGG-GUCUGGUauUGACggaCCu -5'
miRNA: 3'- -CCCGGGGGUCUGGUAUUGACGGACCU- -5'
Results 1 - 5 of 5 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 | |||||||
| 11267 | 3' | -58.1 | NC_003059.1 | + | 7001 | 0.66 | 0.135955 |
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Target: 5'- uGGCCCCCAGAacagauaauucaauaUUAUGGacCUGCCaccUGGGc -3' miRNA: 3'- cCCGGGGGUCU---------------GGUAUU--GACGG---ACCU- -5' |
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| 11267 | 3' | -58.1 | NC_003059.1 | + | 6946 | 0.67 | 0.110835 |
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Target: 5'- aGGGUgCCCagagAGACCGgagGGCUGUCcaaauUGGAg -3' miRNA: 3'- -CCCGgGGG----UCUGGUa--UUGACGG-----ACCU- -5' |
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| 11267 | 3' | -58.1 | NC_003059.1 | + | 5001 | 0.68 | 0.082792 |
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Target: 5'- -uGUCCCCGGGCUgc--CUGUCUGGAa -3' miRNA: 3'- ccCGGGGGUCUGGuauuGACGGACCU- -5' |
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| 11267 | 3' | -58.1 | NC_003059.1 | + | 5312 | 0.69 | 0.07755 |
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Target: 5'- gGGGCCCCaCAGACCA--GCUGg--GGc -3' miRNA: 3'- -CCCGGGG-GUCUGGUauUGACggaCCu -5' |
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| 11267 | 3' | -58.1 | NC_003059.1 | + | 4470 | 1.11 | 2e-05 |
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Target: 5'- gGGGCCCCCAGACCAUAACUGCCUGGAg -3' miRNA: 3'- -CCCGGGGGUCUGGUAUUGACGGACCU- -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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