needle 1_1.fasta 1_3.fasta -gapopen 10.0 -gapextend 0.5 stdout >alig.txt 
needle 1_1.fasta 1_4.fasta -gapopen 10.0 -gapextend 0.5 stdout >>alig.txt
needle 1_3.fasta 1_4.fasta -gapopen 10.0 -gapextend 0.5 stdout >>alig.txt
needle 2_2.fasta 2_3.fasta -gapopen 10.0 -gapextend 0.5 stdout >>alig.txt
needle 2_2.fasta 2_4.fasta -gapopen 10.0 -gapextend 0.5 stdout >>alig.txt
needle 2_3.fasta 2_4.fasta -gapopen 10.0 -gapextend 0.5 stdout >>alig.txt
needle 3_2.fasta 3_3.fasta -gapopen 10.0 -gapextend 0.5 stdout >>alig.txt 
needle 3_2.fasta 3_4.fasta -gapopen 10.0 -gapextend 0.5 stdout >>alig.txt
needle 3_3.fasta 3_4.fasta -gapopen 10.0 -gapextend 0.5 stdout >>alig.txt