I have a bunch of 10 or more very closely related chromosome (DNA) sequences (from different strains) aligned to a "single" reference chromosome. How can I generate multiple sequence alignment along with "reference" of all these sequences without affecting individual alignments to the reference.

What I need is to do is to "add dashes" at relative "insert" positions in other sequences, so that I get a global alignment with respect to reference. "Note. Here I am NOT looking for sequence similarities".

For example: If from position 100 to 125 in sequence No. 1 has an insert. but not in other 9 sequences. In the final expanded alignment I will insert 26 dashes (-) (from 100-125) in the sequences 2 to 10 and in the reference.

And in another situation like above if seq1 has insert at 100-125 and if seq5 has insert from 110-115 and seq8 has insert from 112-119. then I need to insert dashes like above, except in these positions (in seq5: 110-115 and in seq8: 112-119)

Please give me suggestions of logic to script to address this problem. 
 
Input:
Original reference:
CGACAATGCACGACAGAGGAAGCAGAACAGATATTTAGATTGCCTCTCATTTTCTCTCCC

Pairwise alignments:

Ref1: CGACAAT--GCACGACAGAGGAAGCAGAACAGATATTTAGATTGCCTCTCATTTTCTCTCCC
Seq1: CGACAATAAGCACGACAGAGGAAGCAGAACAGATA-----ATTGCCTCTCATTTTC-CTCCC

Ref1: CGACAATGCACGACAGAGGAAGC--AGAACAGATATTTAGATTGCCTCTCATTTTCTCTCCC
Seq2: CGACAAT-CACGACAGAGGAAGCTTAGAACAGATATTTAG---GCCTCTCATTTTCTCTCCC

Ref1: CGACAATGCACGACAGAGGAAG----CAGAACAGATATTTAGATTGCCTCTCA----TTTTCTC
+TCCC
Seq3: CGACAATGCACGACAGAGGAAGTTTTCAGAACAGATATTTAGATTGCCTCTCAAAAATTTTCTC
+TCCC


Output: Final Multiple sequence alignment:

Ref1: CGACAAT--GCACGACAGAGGAAG----C--AGAACAGATATTTAGATTGCCTCTCA----TTT
+TCTCTCCC
Seq1: CGACAATAAGCACGACAGAGGAAG----C--AGAACAGATA-----ATTGCCTCTCA----TTT
+TC-CTCCC
Seq2: CGACAAT---CACGACAGAGGAAG----CTTAGAACAGATATTTAG---GCCTCTCA----TTT
+TCTCTCCC
Seq3: CGACAAT--GCACGACAGAGGAAGTTTTC--AGAACAGATATTTAGATTGCCTCTCAAAAATTT
+TCTCTCCC

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In reply to how to construct multiple sequence alignment from group of pairwise alignments by gudluck

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