#include <algorithm>
#include <iomanip>
#include <iostream>
#include <iterator>
#include <sstream>
#include <string>
#include <unordered_set>
#include <vector>
//#define OUTPUT_BINARY_SEARCH_FOR_PATTERN_MATCH_INDEX_OF_BEGIN
//#define OUTPUT_BINARY_SEARCH_FOR_PATTERN_MATCH_INDEX_OF_END
#define OUTPUT_PATTERN_MATCH_INDEXES
using namespace std;
using Indexes = unordered_set< int >;
using Patterns = vector< string >;
/*
* https://en.wikipedia.org/wiki/Suffix_array#Applications
*
n = len(S)
def search(P):
l = 0; r = n
while l < r:
mid = (l+r) / 2
if P > suffixAt(A[mid]):
l = mid + 1
else:
r = mid
s = l; r = n
while l < r:
mid = (l+r) / 2
if P < suffixAt(A[mid]): <- this comparison should be based on the first |P| characters of suffixAt(A[mid])
r = mid
else:
l = mid + 1
return (s, r)
*/
class SuffixArray {
public:
using VI = vector< int >;
static VI build( const string& S, const int N ){
auto order = sortChars( S, N );
auto classes = computeCharClasses( S, N, order );
for( auto L{ 1 }; L < N; L *= 2 ){
order = sortDoubled( S, N, L, order, classes );
classes = updateClasses( N, L, order, classes );
}
return order;
}
static string to_string( const string& S, const VI& A,
const int L, const int M, const int R,
const string& pattern, const string& cur ){
const auto N = static_cast< int >( A.size() );
ostringstream os;
os << "Pattern: " << pattern << endl
<< "Current: " << cur << endl << endl;
for( auto i{ 0 }; i < N; ++i ){
os << print_LMR( i, L, M, R )
<< "A[ " << setw( 2 ) << i << " ] = " << setw( 2 ) << A[ i ] << " -> " << S.substr( A[ i ] ) << endl;
}
os << print_LMR( N, L, M, R ) << "A[ " << setw( 2 ) << N << " ] = A.end()";
return os.str();
}
private:
static string print_LMR( const int i, const int L, const int M, const int R ){
ostringstream os{ " ", ostringstream::ate };
os << ( ( i == L )? 'L' : ' ' ) << ' '
<< ( ( i == M )? 'M' : ' ' ) << ' '
<< ( ( i == R )? 'R' : ' ' ) << ' ';
return os.str();
}
static VI sortChars( const string& S, const int N ){
const int M = 'z' + 1; // alphabet size
VI order( N ), cnt( M );
for( auto i{ 0 }; i < N; ++i ){
auto c = S[ i ];
++cnt[ c ];
}
for( auto j{ 1 }; j < M; ++j )
cnt[ j ] += cnt[ j-1 ];
for( auto i{ N-1 }; 0 <= i; --i ){
auto c = S[ i ];
--cnt[ c ];
order[ cnt[ c ] ] = i;
}
return order;
}
static VI computeCharClasses( const string& S, const int N, const VI& order ){
VI classes( N, 0 );
for( auto i{ 1 }; i < N; ++i )
if( S[ order[ i ] ] != S[ order[ i-1 ] ] )
classes[ order[ i ] ] = classes[ order[ i-1 ] ] + 1;
else
classes[ order[ i ] ] = classes[ order[ i-1 ] ];
return classes;
}
static VI sortDoubled( const string& S, const int N, const int L, const VI& order, const VI& classes ){
VI next_order( N, 0 ), cnt( N, 0 );
for( auto i{ 0 }; i < N; ++i ){
auto cl = classes[ i ];
++cnt[ cl ];
}
for( auto j{ 1 }; j < N; ++j )
cnt[ j ] += cnt[ j-1 ];
for( auto i{ N-1 }; 0 <= i; --i ){
auto start = ( order[ i ] - L + N ) % N; // start is the begin index of the doubled cyclic shift
auto cl = classes[ start ];
--cnt[ cl ];
next_order[ cnt[ cl ] ] = start;
}
return next_order;
}
static VI updateClasses( const int N, const int L, const VI& order, const VI& classes ){
VI next_classes( N, 0 );
for( auto i{ 1 }; i < N; ++i ){
auto pre = order[ i-1 ], preMid = ( pre + L ) % N,
cur = order[ i ], curMid = ( cur + L ) % N;
if( classes[ pre ] != classes[ cur ] || classes[ preMid ] != classes[ curMid ] )
next_classes[ cur ] = next_classes[ pre ] + 1; // diff equivalence class
else
next_classes[ cur ] = next_classes[ pre ]; // same equivalence class
}
return next_classes;
}
};
int main() {
string S; cin >> S;
S.append( "$" );
const auto N = static_cast< int >( S.size() );
const auto A = SuffixArray::build( S, N );
auto K{ 0 }; cin >> K;
Patterns P; copy_n( istream_iterator< string >( cin ), K, back_inserter( P ) );
Indexes I; {
for( const auto& pattern: P ){
auto L{ 0 }, R{ N };
while( L < R ){
auto M = ( L + R ) / 2;
auto cur = S.substr( A[ M ] );
#ifdef OUTPUT_BINARY_SEARCH_FOR_PATTERN_MATCH_INDEX_OF_BEGIN
cout << SuffixArray::to_string( S, A, L, M, R, pattern, cur ) << endl << endl << endl;
#endif
if( pattern > cur )
L = M + 1;
else
R = M;
}
auto beg{ L };
R = N;
while( L < R ){
auto M = ( L + R ) / 2;
auto cur = S.substr( A[ M ], pattern.size() );
#ifdef OUTPUT_BINARY_SEARCH_FOR_PATTERN_MATCH_INDEX_OF_END
cout << SuffixArray::to_string( S, A, L, M, R, pattern, cur ) << endl << endl << endl;
#endif
if( pattern < cur )
R = M;
else
L = M + 1;
}
auto end{ R };
for(; beg < end; I.insert( A[ beg++ ] ) );
}
}
#ifdef OUTPUT_PATTERN_MATCH_INDEXES
copy( I.begin(), I.end(), ostream_iterator< int >( cout, " " ) ); cout << endl;
#endif
return 0;
}
/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
Problem: find all indexes of the pattern(s) in the genome
Pattern: CCT
Genome: TCCTCTATGAGATCCTATTCTATGAAACCTTCAGACCAAAATTCTCCGGC
012345678901234567890123456789012345678901234567890
0 1 2 3 4 5
* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
*
* Use binary search to find the (beg)in index of the pattern in the genome's suffix array A
*
Pattern: CCT
Current: CTATGAGATCCTATTCTATGAAACCTTCAGACCAAAATTCTCCGGC$
L A[ 0 ] = 50 -> $
A[ 1 ] = 37 -> AAAATTCTCCGGC$
A[ 2 ] = 24 -> AAACCTTCAGACCAAAATTCTCCGGC$
A[ 3 ] = 38 -> AAATTCTCCGGC$
A[ 4 ] = 25 -> AACCTTCAGACCAAAATTCTCCGGC$
A[ 5 ] = 39 -> AATTCTCCGGC$
A[ 6 ] = 34 -> ACCAAAATTCTCCGGC$
A[ 7 ] = 26 -> ACCTTCAGACCAAAATTCTCCGGC$
A[ 8 ] = 32 -> AGACCAAAATTCTCCGGC$
A[ 9 ] = 9 -> AGATCCTATTCTATGAAACCTTCAGACCAAAATTCTCCGGC$
A[ 10 ] = 11 -> ATCCTATTCTATGAAACCTTCAGACCAAAATTCTCCGGC$
A[ 11 ] = 21 -> ATGAAACCTTCAGACCAAAATTCTCCGGC$
A[ 12 ] = 6 -> ATGAGATCCTATTCTATGAAACCTTCAGACCAAAATTCTCCGGC$
A[ 13 ] = 16 -> ATTCTATGAAACCTTCAGACCAAAATTCTCCGGC$
A[ 14 ] = 40 -> ATTCTCCGGC$
A[ 15 ] = 49 -> C$
A[ 16 ] = 36 -> CAAAATTCTCCGGC$
A[ 17 ] = 31 -> CAGACCAAAATTCTCCGGC$
A[ 18 ] = 35 -> CCAAAATTCTCCGGC$
A[ 19 ] = 45 -> CCGGC$
A[ 20 ] = 13 -> CCTATTCTATGAAACCTTCAGACCAAAATTCTCCGGC$
A[ 21 ] = 1 -> CCTCTATGAGATCCTATTCTATGAAACCTTCAGACCAAAATTCTCCGGC$
A[ 22 ] = 27 -> CCTTCAGACCAAAATTCTCCGGC$
A[ 23 ] = 46 -> CGGC$
A[ 24 ] = 19 -> CTATGAAACCTTCAGACCAAAATTCTCCGGC$
M A[ 25 ] = 4 -> CTATGAGATCCTATTCTATGAAACCTTCAGACCAAAATTCTCCGGC$
A[ 26 ] = 14 -> CTATTCTATGAAACCTTCAGACCAAAATTCTCCGGC$
A[ 27 ] = 43 -> CTCCGGC$
A[ 28 ] = 2 -> CTCTATGAGATCCTATTCTATGAAACCTTCAGACCAAAATTCTCCGGC$
A[ 29 ] = 28 -> CTTCAGACCAAAATTCTCCGGC$
A[ 30 ] = 23 -> GAAACCTTCAGACCAAAATTCTCCGGC$
A[ 31 ] = 33 -> GACCAAAATTCTCCGGC$
A[ 32 ] = 8 -> GAGATCCTATTCTATGAAACCTTCAGACCAAAATTCTCCGGC$
A[ 33 ] = 10 -> GATCCTATTCTATGAAACCTTCAGACCAAAATTCTCCGGC$
A[ 34 ] = 48 -> GC$
A[ 35 ] = 47 -> GGC$
A[ 36 ] = 20 -> TATGAAACCTTCAGACCAAAATTCTCCGGC$
A[ 37 ] = 5 -> TATGAGATCCTATTCTATGAAACCTTCAGACCAAAATTCTCCGGC$
A[ 38 ] = 15 -> TATTCTATGAAACCTTCAGACCAAAATTCTCCGGC$
A[ 39 ] = 30 -> TCAGACCAAAATTCTCCGGC$
A[ 40 ] = 44 -> TCCGGC$
A[ 41 ] = 12 -> TCCTATTCTATGAAACCTTCAGACCAAAATTCTCCGGC$
A[ 42 ] = 0 -> TCCTCTATGAGATCCTATTCTATGAAACCTTCAGACCAAAATTCTCCGGC$
A[ 43 ] = 18 -> TCTATGAAACCTTCAGACCAAAATTCTCCGGC$
A[ 44 ] = 3 -> TCTATGAGATCCTATTCTATGAAACCTTCAGACCAAAATTCTCCGGC$
A[ 45 ] = 42 -> TCTCCGGC$
A[ 46 ] = 22 -> TGAAACCTTCAGACCAAAATTCTCCGGC$
A[ 47 ] = 7 -> TGAGATCCTATTCTATGAAACCTTCAGACCAAAATTCTCCGGC$
A[ 48 ] = 29 -> TTCAGACCAAAATTCTCCGGC$
A[ 49 ] = 17 -> TTCTATGAAACCTTCAGACCAAAATTCTCCGGC$
A[ 50 ] = 41 -> TTCTCCGGC$
R A[ 51 ] = A.end()
Pattern: CCT
Current: ATGAGATCCTATTCTATGAAACCTTCAGACCAAAATTCTCCGGC$
L A[ 0 ] = 50 -> $
A[ 1 ] = 37 -> AAAATTCTCCGGC$
A[ 2 ] = 24 -> AAACCTTCAGACCAAAATTCTCCGGC$
A[ 3 ] = 38 -> AAATTCTCCGGC$
A[ 4 ] = 25 -> AACCTTCAGACCAAAATTCTCCGGC$
A[ 5 ] = 39 -> AATTCTCCGGC$
A[ 6 ] = 34 -> ACCAAAATTCTCCGGC$
A[ 7 ] = 26 -> ACCTTCAGACCAAAATTCTCCGGC$
A[ 8 ] = 32 -> AGACCAAAATTCTCCGGC$
A[ 9 ] = 9 -> AGATCCTATTCTATGAAACCTTCAGACCAAAATTCTCCGGC$
A[ 10 ] = 11 -> ATCCTATTCTATGAAACCTTCAGACCAAAATTCTCCGGC$
A[ 11 ] = 21 -> ATGAAACCTTCAGACCAAAATTCTCCGGC$
M A[ 12 ] = 6 -> ATGAGATCCTATTCTATGAAACCTTCAGACCAAAATTCTCCGGC$
A[ 13 ] = 16 -> ATTCTATGAAACCTTCAGACCAAAATTCTCCGGC$
A[ 14 ] = 40 -> ATTCTCCGGC$
A[ 15 ] = 49 -> C$
A[ 16 ] = 36 -> CAAAATTCTCCGGC$
A[ 17 ] = 31 -> CAGACCAAAATTCTCCGGC$
A[ 18 ] = 35 -> CCAAAATTCTCCGGC$
A[ 19 ] = 45 -> CCGGC$
A[ 20 ] = 13 -> CCTATTCTATGAAACCTTCAGACCAAAATTCTCCGGC$
A[ 21 ] = 1 -> CCTCTATGAGATCCTATTCTATGAAACCTTCAGACCAAAATTCTCCGGC$
A[ 22 ] = 27 -> CCTTCAGACCAAAATTCTCCGGC$
A[ 23 ] = 46 -> CGGC$
A[ 24 ] = 19 -> CTATGAAACCTTCAGACCAAAATTCTCCGGC$
R A[ 25 ] = 4 -> CTATGAGATCCTATTCTATGAAACCTTCAGACCAAAATTCTCCGGC$
Pattern: CCT
Current: CCGGC$
L A[ 13 ] = 16 -> ATTCTATGAAACCTTCAGACCAAAATTCTCCGGC$
A[ 14 ] = 40 -> ATTCTCCGGC$
A[ 15 ] = 49 -> C$
A[ 16 ] = 36 -> CAAAATTCTCCGGC$
A[ 17 ] = 31 -> CAGACCAAAATTCTCCGGC$
A[ 18 ] = 35 -> CCAAAATTCTCCGGC$
M A[ 19 ] = 45 -> CCGGC$
A[ 20 ] = 13 -> CCTATTCTATGAAACCTTCAGACCAAAATTCTCCGGC$
A[ 21 ] = 1 -> CCTCTATGAGATCCTATTCTATGAAACCTTCAGACCAAAATTCTCCGGC$
A[ 22 ] = 27 -> CCTTCAGACCAAAATTCTCCGGC$
A[ 23 ] = 46 -> CGGC$
A[ 24 ] = 19 -> CTATGAAACCTTCAGACCAAAATTCTCCGGC$
R A[ 25 ] = 4 -> CTATGAGATCCTATTCTATGAAACCTTCAGACCAAAATTCTCCGGC$
Pattern: CCT
Current: CCTTCAGACCAAAATTCTCCGGC$
L A[ 20 ] = 13 -> CCTATTCTATGAAACCTTCAGACCAAAATTCTCCGGC$
A[ 21 ] = 1 -> CCTCTATGAGATCCTATTCTATGAAACCTTCAGACCAAAATTCTCCGGC$
M A[ 22 ] = 27 -> CCTTCAGACCAAAATTCTCCGGC$
A[ 23 ] = 46 -> CGGC$
A[ 24 ] = 19 -> CTATGAAACCTTCAGACCAAAATTCTCCGGC$
R A[ 25 ] = 4 -> CTATGAGATCCTATTCTATGAAACCTTCAGACCAAAATTCTCCGGC$
Pattern: CCT
Current: CCTCTATGAGATCCTATTCTATGAAACCTTCAGACCAAAATTCTCCGGC$
L A[ 20 ] = 13 -> CCTATTCTATGAAACCTTCAGACCAAAATTCTCCGGC$
M A[ 21 ] = 1 -> CCTCTATGAGATCCTATTCTATGAAACCTTCAGACCAAAATTCTCCGGC$
R A[ 22 ] = 27 -> CCTTCAGACCAAAATTCTCCGGC$
Pattern: CCT
Current: CCTATTCTATGAAACCTTCAGACCAAAATTCTCCGGC$
L M A[ 20 ] = 13 -> CCTATTCTATGAAACCTTCAGACCAAAATTCTCCGGC$
R A[ 21 ] = 1 -> CCTCTATGAGATCCTATTCTATGAAACCTTCAGACCAAAATTCTCCGGC$
beg A[ 20 ] = 13 -> CCTATTCTATGAAACCTTCAGACCAAAATTCTCCGGC$
*
* Found the (beg)in index of the pattern in the genome's suffix array A
*
* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
*
* Use binary search to find the end index of the pattern in the genome's suffix array A
*
Pattern: CCT
Current: GGC
L A[ 20 ] = 13 -> CCTATTCTATGAAACCTTCAGACCAAAATTCTCCGGC$
A[ 21 ] = 1 -> CCTCTATGAGATCCTATTCTATGAAACCTTCAGACCAAAATTCTCCGGC$
A[ 22 ] = 27 -> CCTTCAGACCAAAATTCTCCGGC$
A[ 23 ] = 46 -> CGGC$
A[ 24 ] = 19 -> CTATGAAACCTTCAGACCAAAATTCTCCGGC$
A[ 25 ] = 4 -> CTATGAGATCCTATTCTATGAAACCTTCAGACCAAAATTCTCCGGC$
A[ 26 ] = 14 -> CTATTCTATGAAACCTTCAGACCAAAATTCTCCGGC$
A[ 27 ] = 43 -> CTCCGGC$
A[ 28 ] = 2 -> CTCTATGAGATCCTATTCTATGAAACCTTCAGACCAAAATTCTCCGGC$
A[ 29 ] = 28 -> CTTCAGACCAAAATTCTCCGGC$
A[ 30 ] = 23 -> GAAACCTTCAGACCAAAATTCTCCGGC$
A[ 31 ] = 33 -> GACCAAAATTCTCCGGC$
A[ 32 ] = 8 -> GAGATCCTATTCTATGAAACCTTCAGACCAAAATTCTCCGGC$
A[ 33 ] = 10 -> GATCCTATTCTATGAAACCTTCAGACCAAAATTCTCCGGC$
A[ 34 ] = 48 -> GC$
M A[ 35 ] = 47 -> GGC$
A[ 36 ] = 20 -> TATGAAACCTTCAGACCAAAATTCTCCGGC$
A[ 37 ] = 5 -> TATGAGATCCTATTCTATGAAACCTTCAGACCAAAATTCTCCGGC$
A[ 38 ] = 15 -> TATTCTATGAAACCTTCAGACCAAAATTCTCCGGC$
A[ 39 ] = 30 -> TCAGACCAAAATTCTCCGGC$
A[ 40 ] = 44 -> TCCGGC$
A[ 41 ] = 12 -> TCCTATTCTATGAAACCTTCAGACCAAAATTCTCCGGC$
A[ 42 ] = 0 -> TCCTCTATGAGATCCTATTCTATGAAACCTTCAGACCAAAATTCTCCGGC$
A[ 43 ] = 18 -> TCTATGAAACCTTCAGACCAAAATTCTCCGGC$
A[ 44 ] = 3 -> TCTATGAGATCCTATTCTATGAAACCTTCAGACCAAAATTCTCCGGC$
A[ 45 ] = 42 -> TCTCCGGC$
A[ 46 ] = 22 -> TGAAACCTTCAGACCAAAATTCTCCGGC$
A[ 47 ] = 7 -> TGAGATCCTATTCTATGAAACCTTCAGACCAAAATTCTCCGGC$
A[ 48 ] = 29 -> TTCAGACCAAAATTCTCCGGC$
A[ 49 ] = 17 -> TTCTATGAAACCTTCAGACCAAAATTCTCCGGC$
A[ 50 ] = 41 -> TTCTCCGGC$
R A[ 51 ] = A.end()
Pattern: CCT
Current: CTC
L A[ 20 ] = 13 -> CCTATTCTATGAAACCTTCAGACCAAAATTCTCCGGC$
A[ 21 ] = 1 -> CCTCTATGAGATCCTATTCTATGAAACCTTCAGACCAAAATTCTCCGGC$
A[ 22 ] = 27 -> CCTTCAGACCAAAATTCTCCGGC$
A[ 23 ] = 46 -> CGGC$
A[ 24 ] = 19 -> CTATGAAACCTTCAGACCAAAATTCTCCGGC$
A[ 25 ] = 4 -> CTATGAGATCCTATTCTATGAAACCTTCAGACCAAAATTCTCCGGC$
A[ 26 ] = 14 -> CTATTCTATGAAACCTTCAGACCAAAATTCTCCGGC$
M A[ 27 ] = 43 -> CTCCGGC$
A[ 28 ] = 2 -> CTCTATGAGATCCTATTCTATGAAACCTTCAGACCAAAATTCTCCGGC$
A[ 29 ] = 28 -> CTTCAGACCAAAATTCTCCGGC$
A[ 30 ] = 23 -> GAAACCTTCAGACCAAAATTCTCCGGC$
A[ 31 ] = 33 -> GACCAAAATTCTCCGGC$
A[ 32 ] = 8 -> GAGATCCTATTCTATGAAACCTTCAGACCAAAATTCTCCGGC$
A[ 33 ] = 10 -> GATCCTATTCTATGAAACCTTCAGACCAAAATTCTCCGGC$
A[ 34 ] = 48 -> GC$
R A[ 35 ] = 47 -> GGC$
Pattern: CCT
Current: CGG
L A[ 20 ] = 13 -> CCTATTCTATGAAACCTTCAGACCAAAATTCTCCGGC$
A[ 21 ] = 1 -> CCTCTATGAGATCCTATTCTATGAAACCTTCAGACCAAAATTCTCCGGC$
A[ 22 ] = 27 -> CCTTCAGACCAAAATTCTCCGGC$
M A[ 23 ] = 46 -> CGGC$
A[ 24 ] = 19 -> CTATGAAACCTTCAGACCAAAATTCTCCGGC$
A[ 25 ] = 4 -> CTATGAGATCCTATTCTATGAAACCTTCAGACCAAAATTCTCCGGC$
A[ 26 ] = 14 -> CTATTCTATGAAACCTTCAGACCAAAATTCTCCGGC$
R A[ 27 ] = 43 -> CTCCGGC$
Pattern: CCT
Current: CCT
L A[ 20 ] = 13 -> CCTATTCTATGAAACCTTCAGACCAAAATTCTCCGGC$
M A[ 21 ] = 1 -> CCTCTATGAGATCCTATTCTATGAAACCTTCAGACCAAAATTCTCCGGC$
A[ 22 ] = 27 -> CCTTCAGACCAAAATTCTCCGGC$
R A[ 23 ] = 46 -> CGGC$
Pattern: CCT
Current: CCT
L M A[ 22 ] = 27 -> CCTTCAGACCAAAATTCTCCGGC$
R A[ 23 ] = 46 -> CGGC$
end A[ 23 ] = 46 -> CGGC$
*
* Found the end index of the pattern in the genome's suffix array A
*
* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
*
* The pattern match indexes are the values in A[ beg : end )
*
* i.e. from A[ beg ] inclusive to A[ end ] non-inclusive
*
Pattern: CCT
beg A[ 20 ] = 13 -> CCTATTCTATGAAACCTTCAGACCAAAATTCTCCGGC$
A[ 21 ] = 1 -> CCTCTATGAGATCCTATTCTATGAAACCTTCAGACCAAAATTCTCCGGC$
A[ 22 ] = 27 -> CCTTCAGACCAAAATTCTCCGGC$
end A[ 23 ] = 46 -> CGGC$
Indexes: 1 13 27
* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
Summary:
Problem: find all indexes of the pattern(s) in the genome
Pattern: CCT
CCT CCT CCT
Genome: TCCTCTATGAGATCCTATTCTATGAAACCTTCAGACCAAAATTCTCCGGC
^^^ ^^^ ^^^
012345678901234567890123456789012345678901234567890
0 1 2 3 4 5
Indexes: 1 13 27
* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */
