To change the numbering of a MacVector sequence hover the mouse over the ‘red’ cross (or number) that appears at the beginning of a sequence. This will change to a hand. Double click and enter the new start number in the dialog that appears. You may also drag the red cross to a place in the sequence which will be reset to be base ‘0’.
By default when you copy a smaller sequence from a region of a larger sequence then the numbering of the larger sequence is retained.
For example if you selected and copied 1,000,000 to 1,000,100 from a larger sequence and pasted it in a new sequence window then your new sequence would be 101 bases long and the first base would start numbering from 1,000,000.