Labeling this number of sequences as 'positive' was found by AME to be optimal (or your primary sequence file contains this number of sequences and you also provided a control sequence file). The sequences were chosen as described above under "Labeling positives".

Labeling this number of sequences as 'negative' was found by AME to be optimal (or you provided a control sequence file containing this number of sequences). The sequences are those remaining after the 'positive' sequences were chosen as described above under "Labeling positives".

The number (percentage) of sequences labeled as 'positive' (Pos) and classified as 'positive' (TP),
     %TP = 100 * TP/Pos.
Labeling of sequences as 'positive' is described in the help bubble for "Pos". Classification is described above under "Classifying positives".

The number (percentage) of sequences labeled as 'negative' (Neg) but classified as 'positive' (FP),
     %FP = 100 * FP/Neg.
Labeling of sequences as 'negative' is described in the help bubble for "Neg". Classification is described above under "Classifying positives".

The (optimal) score threshold for labeling sequences as 'positive' determined by AME. (See the note about "Labeling positives" in the section above.)

The (optimal) score threshold for classifying sequences as 'positive' determined by AME (or provided by you using --hit-odds-fraction or --fasta-threshold).
By default, the true positive and false positive sequences are those with sequence motif scores ≥ the value shown.
If you specified --poslist pwm, then the true positive and false positive sequences are those with FASTA scores ≤ the value shown.

The value of Pearson's correlation coefficient (ρ). It varies between -1 and +1. High values of ρ indicate strong correlation between the sequence motif scores and the sequence FASTA scores. Note that positive ρ means that sequence motif scores go up when sequence FASTA scores go down. The p-value of this method is the probability that ρ is at least as large as the observed value assuming there is no relation between the scores.

The value of Spearman's rank correlation coefficient (ρ). It varies between -1 and +1. High values of ρ indicate strong correlation between the sequence motif score ranks and the sequence FASTA score ranks. Note that positive ρ means that sequence motif scores go up when sequence FASTA scores go down. The p-value of this method is the probability that ρ is at least as large as the observed value assuming there is no relation between the scores.

The value of the mean squared error of the linear regression of X vs Y.

The slope of the regression line: Y = mX + b.

The Y-intercept of the regression line: Y = mX + b.