#=======================================
#
# Aligned_sequences: 2
# 1: 11111111
# 2: 00000000
# Matrix: EDNAFULL
# Gap_penalty: 10.0
# Extend_penalty: 0.5
#
# Length: 3678
# Identity:    3387/3678 (92.1%)
# Similarity:  3387/3678 (92.1%)
# Gaps:         285/3678 ( 7.7%)
# Score: 16911.0
# 
#
#=======================================
11111111     751 AGCACTGGTACCTTAGTGGTAAATGAGAAGATGAAAGAAATGGATCAGAA    800
                     ||||||||||||||||||||||||||||||||||.|||||||||||||||
00000000     466 AGCACTGGTACCTTAGTGGTAAATGAGAAGATGAGAGAAATGGATCAGAA    515

11111111     801 ATACCAGGTTGCAGAGAAGACCAAATCAGCATTAGCAGCTGCAGAACAGA    850
                     ||||||||||||||||||||||||||||||||||||||||||||||||||
00000000     516 ATACCAGGTTGCAGAGAAGACCAAATCAGCATTAGCAGCTGCAGAACAGA    565

11111111     851 CAGTCTCTACTGCTGGCTCTGCAATCATGAGTAACAGATACATCCTTACA    900
                     ||||||||||||||||||||||||||||||||||||||||||||||||||
00000000     566 CAGTCTCTACTGCTGGCTCTGCAATCATGAGTAACAGATACATCCTTACA    615

for example,I want to get SNPs the locations,may be in my result,i also need to get gaps location. but, i couldn't think a way to find them. could you help me?

The format is false,i give it in photo.