You can go for BioEdit, Chromas, etc for the purpose.

What about AliView (http://www.ormbunkar.se/aliview/)?

U can try ugene http://ugene.unipro.ru/documentation/manual/alignment_editor/overview/features.html

You can select BioEdit for doing this kinda work. It will also give you many more features.

Hi

Bioedit is better and user-friendly

Dear friend

please use SSE software for edit any file of biological data. if you need any help about this, please connect with me,

http://www.sequence-alignment.com/sequence-alignment-software.html

MEGA

http://www.megasoftware.net/

go for Bioedit

Depending on how clean your chromatograms are you could use BioEdit since it is user friendly. If the sequence are of lower quality, manual editing using Chromas Lite would be a better option

if you are talking about complete genomes, I`,m not sure Bioedit or MEGA is a choice. For small sequences - definitely yes (for Windows and Linux): Bioedit for manipulations, MEGA for aligning and treeing. For the purposes you talked about my suggestion will be Mauve or Tablet

sequence scanner and bioedit software ..... both are easy to get and easy to use

You can prefer BioEdit, it is better and user friendly.  

It sounds like you might be doing some sort of finishing work. If that's true, you could also consider GAP4: http://staden.sourceforge.net/

Also, PBJelly could be an option. Although it is developped to map PacBio reads to high quality genome, you can map your assembly onto your chosen reference to correct the gaps:

http://sourceforge.net/p/pb-jelly/wiki/Home/

You can use BioEdit