my @array1=(
  [qw(small_motif_b 789 799)],
  [qw(small_motif_a 811 821)],
  [qw(small_motif_i 822 832)],
  [qw(tall_motif_a 833 880)],
  [qw(small_motif_a 881 891)],
  [qw(small_motif_b 892 902)],
  [qw(small_motif_a 903 913)],
  [qw(tall_motif_b 914 961)],
  [qw(small_motif_a 962 972)],
  [qw(tall_motif_c 973 1020)],
);

my @array2=(
  [qw(NC_010109.1 NTRFinder . . . ID=NTR-a1;Parent=NTR-a;Name=motif_small_b)],
  [qw(NC_010109.1 NTRFinder . . . ID=NTR-a2;Parent=NTR-a;Name=motif_small_a)],
  [qw(NC_010109.1 NTRFinder . . . ID=NTR-a3;Parent=NTR-a;Name=motif_small_i)],
  [qw(NC_010109.1 NTRFinder . . . ID=NTR-a4;Parent=NTR-a;Name=tall_motif_a)],
  [qw(NC_010109.1 NTRFinder . . . ID=NTR-a5;Parent=NTR-a;Name=motif_small_a)],
  [qw(NC_010109.1 NTRFinder . . . ID=NTR-a6;Parent=NTR-a;Name=motif_small_b)],
  [qw(NC_010109.1 NTRFinder . . . ID=NTR-a7;Parent=NTR-a;Name=motif_small_a)],
  [qw(NC_010109.1 NTRFinder . . . ID=NTR-a8;Parent=NTR-a;Name=tall_motif_b)],
  [qw(NC_010109.1 NTRFinder . . . ID=NTR-a9;Parent=NTR-a;Name=motif_small_a)],
  [qw(NC_010109.1 NTRFinder . . . ID=NTR-a10;Parent=NTR-a;Name=tall_motif_c)],
);

for my $pos (0..$#array2)
{
  splice(@{$array2[$pos]},2,0,@{$array1[$pos]});
}