+ if (m->debug) { m->mothurOut("[DEBUG]: " + seq.getName() + " length = " + toString(seq.getAligned().length())); m->mothurOutEndLine();}
+ if (seq.getAligned().length() != alignmentLength) { m->mothurOut("[ERROR]: Sequences are not all the same length, please correct."); m->mothurOutEndLine(); m->control_pressed = true; }