function y = sequencing_flags(NTI,SEQ,truncation,sequence_start,indices)

fid1 = fopen(NTI,'rt');
fid2 = fopen(SEQ,'rt');

NTI_file = fgetl(fid1);
SEQ_file = fgetl(fid2);

sequence_start = sequence_start-1

seq_adjusted_index = truncation - sequence_start

sequence_flags = {}

for i = 1:length(indices),
    a = indices(i);
    sequence_flags{i,1} = a+seq_adjusted_index;
    sequence_flags{i,2} = a;
    sequence_flags{i,3} = NTI_file(a);
    sequence_flags{i,4} = SEQ_file(a+seq_adjusted_index);
end

sequence_flags{1,1}

header1 = sprintf('%s','{| {{table}}')
head_length1 = length(header1)
header(1,1:head_length1) = header1
    
header2 = sprintf('%s','| align="center" style="background:#f0f0f0;|Base Number (Sequence File Annotation)');
head_length2 = length(header2)
header(2,1:head_length2) = header2
    
header3 = sprintf('%s','| align="center" style="background:#f0f0f0;"|Base Number (Vector NTI File Annotation)');
head_length3 = length(header3)
header(3,1:head_length3) = header3
    
header4 = sprintf('%s','| align="center" style="background:#f0f0f0;"|Theoretical Base');
head_length4 = length(header4)
header(4,1:head_length4) = header4
    
header5 = sprintf('%s','| align="center" style="background:#f0f0f0;"|Read Base');
head_length5 = length(header5)
header(5,1:head_length5) = header5
    
header6 = sprintf('%s','| align="center" style="background:#f0f0f0;"|Notes');
head_length6 = length(header6)
header(6,1:head_length6) = header6


for i=1:length(indices)
    a = sprintf('%s %d %s %d %s %d %s %d %s','|',sequence_flags{i,1},'||',sequence_flags{i,2},'||',sequence_flags{i,3},'||',sequence_flags{i,4},'||');
    b = length(a);
    data(i+6,1:b) = a;
    final = i+6
end

footer = sprintf('%s','|}');
foot_length = length(footer);

data(1,1:head_length1) = header1
data(2,1:head_length2) = header2
data(3,1:head_length3) = header3
data(4,1:head_length4) = header4
data(5,1:head_length5) = header5
data(6,1:head_length6) = header6

data(final+1,1:foot_length) = footer;

y = data