Design Array - OutputsThe results are sent to the e-mail address provided by the user. The tab-delimited text attachment shows the results in detail using a table of multiple columns. The user can open this file with a spreadsheet program, such as MS Excel, for analyzing the results.
Name of the target group according each unique identifier in the FASTA file.
Starting position of the target site within the respective consensus sequence. The consensus sequence position does not include gap positions.
Length of the target site in nucleotides, which will be between the minimum and maximum set by the user. Note that the actual probe sequence is longer because it includes in a poly-T spacer that separates the probes from the microarray substrate. The number of T's in the spacer is set so that the probe sequence can be synthesized within 148 design cycles.
Starting and ending positions of the probe in the alignment including gap positions.
Number of probe permutations required to represent the target site, which is less than or equal to the maximum number of permutations set by the user.
Measurement of the specificity of the probe to the target group. A score of zero is the highest specificity, while a more negative score is less specific. Only the top scoring probes are included in the outputs.
The predicted formamide melt point (%; vol/vol) of the probe, which is between the minimum and maximum melt points set by the user. If more than one probe permutation is given then only the lowest melt point is listed.
The percent hybridization efficiency of probe at a formamide concentration 5% below the minimum melt point specified by the user. This is the concentration (vol/vol) of formamide that should be used in the hybridization buffer along with 1M [Na+]. If more than one probe permutation is given then only the lowest hybridization efficiency is listed.
Perfect match target sequence of the probe permutation(s), which is the reverse complement of the probe sequence(s).
Comma-separated list of probes giving every permutation of the target site. The probes should be fabricated onto the microarray as given (5’ to 3’).
Lists non-target groups that are predicted to cross-hybridize with the probe(s), and their respective hybridization efficiency.