Such misalignments result from a set of factors that we have no control over, such as: sequencing errors, SNPs, indels and/or RefEX size, combined with controllable factors, such as read length, SZ r (longer readsare less likely to be misaligned) and alignment approximation.
Such misalignments result from a set of factors that we have no control over, such as: sequencing errors, SNPs, indels and/or RefEX size, combined with controllable factors, such as read length, SZr (longer readsare less likely to be misaligned) and alignment approximation.
A repeated-measures, mixed-factor 2 (congruency: congruent, incongruent) × 2 (alignment: aligned, misaligned) × 2 (expertise: expert, novice) analysis of variance (ANOVA) was performed for experiment 1.
The repeated-measures, mixed-factor 2 (congruency: congruent, incongruent) × 2 (alignment: aligned, misaligned) × 2 (expertise: expert, novice) ANOVA confirmed this result.
The factors were priming level (global, local) × alignment (aligned, misaligned) × congruency (congruent, incongruent).
There were 20 trials for each combination of cued half (top or bottom), trial type (match or non-match), side congruency (congruent or incongruent), and alignment (aligned or misaligned), resulting in 320 trials total.
This effect was even more pronounced when larger fractions of the multiple sequence alignment were misaligned.
Alignments were examined for misaligned areas; these were aligned by eye or excluded.
Our method is also different from the multiple genome alignment based methods, in that we use local alignments, which enables us to identify conserved TFBSs and CRMs that may be "misaligned" in the multiple alignments [ 26].
Experiment 1 and Experiment 2 were both 2 × 2 × 2 mixed designs, where the within-subjects factors were side congruency (congruent or incongruent) and alignment (halves were aligned or misaligned).
The two best examples of this phenomenon are the two conserved regions (the bsAlt region in vertebrates and a Kruppel site in Drosophila) that were misaligned in the multiz alignments.
