String sqstring = sq.getSequenceAsString(start, end + 1);
seq = new Sequence(newName,
AlignSeq.extractGaps(jalview.util.Comparison.GapChars, sqstring));
String sqstring = sq.getSequenceAsString(start, end + 1);
seq = new Sequence(newName,
AlignSeq.extractGaps(jalview.util.Comparison.GapChars, sqstring));