code: public boolean isSignificant() {
  
  		// In any case if the order is 1 it is asymmetric
  		if (numRepeats < 2)
  			return false;
  
  		// If the TM-Score before refinement is below the threshold
  		if (selfAlignment.getTMScore() < params.getUnrefinedScoreThreshold())
  			return false;
  
  		// If the refinement was attempted
  		if (params.getRefineMethod() != RefineMethod.NOT_REFINED) {
  			// Check for minimum length
  			if (multipleAlignment == null || multipleAlignment.getCoreLength() < params.getMinCoreLength())
  				return false;
  			// Allow 90% of original TM-Score theshold
  			if (multipleAlignment.getScore(MultipleAlignmentScorer.AVGTM_SCORE) < params
  					.getRefinedScoreThreshold())
  				return false;
  			return true;
  		}
  
  		return true;
  	}
docs: Conditions checked are: score above the threshold, number of repeats
  higher than 1 and refinement succeeded.
  
  @return true if significant, false otherwise