#define NULL ((void *)0)
typedef unsigned long size_t; // Customize by platform.
typedef long intptr_t;
typedef unsigned long uintptr_t;
typedef long scalar_t__; // Either arithmetic or pointer type.
/* By default, we understand bool (as a convenience). */
typedef int bool;
#define false 0
#define true 1

/* Forward declarations */

/* Type definitions */

/* Variables and functions */
scalar_t__ calloc(int, int);
int /*<<< orphan*/ free(unsigned long long *);
int /*<<< orphan*/ printf(char *, char, ...);
int Edit_Distance_multiple_word_NoEndPenaltySeq1(char *stringN, char *stringM,
                                                 int N, int M) {
  int i, j;
  unsigned long long int *matchA;
  unsigned long long int *matchC;
  unsigned long long int *matchG;
  unsigned long long int *matchT;
  unsigned long long int *matchN;
  unsigned long long int *matchVector;
  unsigned long long int bitmask;
  unsigned long long int matchString;
  unsigned long long int *P_D;
  unsigned long long int *P_S_or_P_D;
  unsigned long long int M_m;
  unsigned long long int R_IS;
  unsigned long long int not_M_I;
  unsigned long long int not_M_I_xor_P_D;
  unsigned long long int VC_0;
  unsigned long long int VC_plus_1;
  unsigned long long int VC_0_shift;
  unsigned long long int VC_plus_1_shift;
  unsigned long long int sum;
  unsigned long long int sum_and_R_IS;
  unsigned long long int highBitMask64 = 0x8000000000000000;
  unsigned long long int carryBitSum;
  unsigned long long int carryBitVC_plus_1_shift;
  unsigned long long int carryBitVC_0_shift;
  unsigned long long int oldCarryBitVC_plus_1_shift;
  unsigned long long int oldCarryBitVC_0_shift;
  unsigned long long int P_DErase;
  unsigned long long int P_IErase;
  unsigned long long int mask;
  int Score;
  int bestFinalRowScore;
  int nWords;
  int integerPart;
  int NWords;
  if (M == 0)
    return (0);
  if (N > 64 - 1) {
    integerPart = (N - 64 + 1) / 64;
    nWords =
        (N - 64 + 1 - 64 * integerPart) > 0 ? integerPart + 2 : integerPart + 1;
  } else
    nWords = 1;
  NWords = nWords;
  matchA =
      (unsigned long long int *)calloc(NWords, sizeof(unsigned long long int));
  matchC =
      (unsigned long long int *)calloc(NWords, sizeof(unsigned long long int));
  matchG =
      (unsigned long long int *)calloc(NWords, sizeof(unsigned long long int));
  matchT =
      (unsigned long long int *)calloc(NWords, sizeof(unsigned long long int));
  matchN =
      (unsigned long long int *)calloc(NWords, sizeof(unsigned long long int));
  P_D =
      (unsigned long long int *)calloc(NWords, sizeof(unsigned long long int));
  P_S_or_P_D =
      (unsigned long long int *)calloc(NWords, sizeof(unsigned long long int));
  for (j = 0; j < NWords; j++) {
    bitmask = 0x0000000000000001;
    matchA[j] = 0x0000000000000000;
    matchC[j] = 0x0000000000000000;
    matchG[j] = 0x0000000000000000;
    matchT[j] = 0x0000000000000000;
    matchN[j] = 0x0000000000000000;
    for (i = j * 64; i < (j + 1) * 64; i++) {
      if (i <= N) {
        if (i || j) {
          switch (stringN[i - 1]) {
          case 'A':
            matchA[j] |= bitmask;
            break;
          case 'C':
            matchC[j] |= bitmask;
            break;
          case 'G':
            matchG[j] |= bitmask;
            break;
          case 'T':
            matchT[j] |= bitmask;
            break;
          case 'N':
            matchN[j] |= bitmask;
            break;
          default:
            printf(
                "\nError, non-ACGTN character read at position %d in string:%c",
                i, stringN[i]);
            free(matchA);
            free(matchC);
            free(matchG);
            free(matchT);
            free(matchN);
            free(P_D);
            free(P_S_or_P_D);
            ;
            return (-1);
            break;
          }
        }
        bitmask <<= 1;
      }
    }
  }
  P_D[0] = 1;
  P_S_or_P_D[0] = 1;
  for (i = 0; i < M; i++) {
    carryBitSum = 0x0000000000000000;
    carryBitVC_plus_1_shift = 0x0000000000000001;
    carryBitVC_0_shift = 0x0000000000000000;
    switch (stringM[i]) {
    case 'A':
      matchVector = matchA;
      break;
    case 'C':
      matchVector = matchC;
      break;
    case 'G':
      matchVector = matchG;
      break;
    case 'T':
      matchVector = matchT;
      break;
    case 'N':
      matchVector = matchN;
      break;
    default:
      printf("\nError, non-ACGTN character read in string:%c", stringM[i]);
      free(matchA);
      free(matchC);
      free(matchG);
      free(matchT);
      free(matchN);
      free(P_D);
      free(P_S_or_P_D);
      ;
      return (-1);
      break;
    }
    for (j = 0; j < NWords; j++) {
      oldCarryBitVC_plus_1_shift = carryBitVC_plus_1_shift;
      oldCarryBitVC_0_shift = carryBitVC_0_shift;
      matchString = matchVector[j];
      M_m = matchString | P_D[j];
      R_IS = ~M_m;
      not_M_I = R_IS | P_S_or_P_D[j];
      not_M_I_xor_P_D = not_M_I ^ P_D[j];
      sum = not_M_I + P_S_or_P_D[j] + carryBitSum;
      if (sum < not_M_I)
        carryBitSum = 1;
      sum_and_R_IS = sum & R_IS;
      VC_0 = sum_and_R_IS ^ not_M_I_xor_P_D;
      VC_plus_1 = P_D[j] | (sum_and_R_IS & P_S_or_P_D[j]);
      carryBitVC_0_shift = (VC_0 & highBitMask64) >> 63;
      carryBitVC_plus_1_shift = (VC_plus_1 & highBitMask64) >> 63;
      VC_0_shift = (VC_0 << 1) + oldCarryBitVC_0_shift;
      VC_plus_1_shift = (VC_plus_1 << 1) + oldCarryBitVC_plus_1_shift;
      P_D[j] = M_m & VC_plus_1_shift;
      P_S_or_P_D[j] = VC_plus_1_shift | (M_m & VC_0_shift);
    }
  }
  mask = 0x0000000000000001;
  bestFinalRowScore = M;
  Score = M;
  for (j = 0; j < NWords; j++) {
    P_DErase = P_D[j];
    P_IErase = ~(P_S_or_P_D[j]);
    for (i = 0; i < 64; i++) {
      if (i | j) {
        Score -= (int)P_DErase & mask;
        Score += (int)P_IErase & mask;
        if (Score < bestFinalRowScore)
          bestFinalRowScore = Score;
      }
      P_DErase >>= 1;
      P_IErase >>= 1;
    }
  }
  free(matchA);
  free(matchC);
  free(matchG);
  free(matchT);
  free(matchN);
  free(P_D);
  free(P_S_or_P_D);
  ;
  return (bestFinalRowScore);
}


x86 assembly (clang, -O0):
<Edit_Distance_multiple_word_NoEndPenaltySeq1>:
push   %rbp
mov    %rsp,%rbp
sub    $0x140,%rsp
mov    %rdi,-0x10(%rbp)
mov    %rsi,-0x18(%rbp)
mov    %edx,-0x1c(%rbp)
mov    %ecx,-0x20(%rbp)
movabs $0x8000000000000000,%rax
mov    %rax,-0xd0(%rbp)
cmpl   $0x0,-0x20(%rbp)
jne    1170 <Edit_Distance_multiple_word_NoEndPenaltySeq1+0x40>
movl   $0x0,-0x4(%rbp)
jmp    190b <Edit_Distance_multiple_word_NoEndPenaltySeq1+0x7db>
cmpl   $0x3f,-0x1c(%rbp)
jle    11e2 <Edit_Distance_multiple_word_NoEndPenaltySeq1+0xb2>
mov    -0x1c(%rbp),%eax
sub    $0x40,%eax
add    $0x1,%eax
mov    $0x40,%ecx
cltd
idiv   %ecx
mov    %eax,-0x120(%rbp)
mov    -0x1c(%rbp),%eax
sub    $0x40,%eax
add    $0x1,%eax
mov    -0x120(%rbp),%ecx
shl    $0x6,%ecx
sub    %ecx,%eax
cmp    $0x0,%eax
jle    11c2 <Edit_Distance_multiple_word_NoEndPenaltySeq1+0x92>
mov    -0x120(%rbp),%eax
add    $0x2,%eax
mov    %eax,-0x128(%rbp)
jmp    11d1 <Edit_Distance_multiple_word_NoEndPenaltySeq1+0xa1>
mov    -0x120(%rbp),%eax
add    $0x1,%eax
mov    %eax,-0x128(%rbp)
mov    -0x128(%rbp),%eax
mov    %eax,-0x11c(%rbp)
jmp    11ec <Edit_Distance_multiple_word_NoEndPenaltySeq1+0xbc>
movl   $0x1,-0x11c(%rbp)
mov    -0x11c(%rbp),%eax
mov    %eax,-0x124(%rbp)
mov    -0x124(%rbp),%edi
mov    $0x8,%esi
call   1050 <calloc@plt>
mov    %rax,-0x30(%rbp)
mov    -0x124(%rbp),%edi
mov    $0x8,%esi
call   1050 <calloc@plt>
mov    %rax,-0x38(%rbp)
mov    -0x124(%rbp),%edi
mov    $0x8,%esi
call   1050 <calloc@plt>
mov    %rax,-0x40(%rbp)
mov    -0x124(%rbp),%edi
mov    $0x8,%esi
call   1050 <calloc@plt>
mov    %rax,-0x48(%rbp)
mov    -0x124(%rbp),%edi
mov    $0x8,%esi
call   1050 <calloc@plt>
mov    %rax,-0x50(%rbp)
mov    -0x124(%rbp),%edi
mov    $0x8,%esi
call   1050 <calloc@plt>
mov    %rax,-0x70(%rbp)
mov    -0x124(%rbp),%edi
mov    $0x8,%esi
call   1050 <calloc@plt>
mov    %rax,-0x78(%rbp)
movl   $0x0,-0x28(%rbp)
mov    -0x28(%rbp),%eax
cmp    -0x124(%rbp),%eax
jge    148b <Edit_Distance_multiple_word_NoEndPenaltySeq1+0x35b>
movq   $0x1,-0x60(%rbp)
mov    -0x30(%rbp),%rax
movslq -0x28(%rbp),%rcx
movq   $0x0,(%rax,%rcx,8)
mov    -0x38(%rbp),%rax
movslq -0x28(%rbp),%rcx
movq   $0x0,(%rax,%rcx,8)
mov    -0x40(%rbp),%rax
movslq -0x28(%rbp),%rcx
movq   $0x0,(%rax,%rcx,8)
mov    -0x48(%rbp),%rax
movslq -0x28(%rbp),%rcx
movq   $0x0,(%rax,%rcx,8)
mov    -0x50(%rbp),%rax
movslq -0x28(%rbp),%rcx
movq   $0x0,(%rax,%rcx,8)
mov    -0x28(%rbp),%eax
shl    $0x6,%eax
mov    %eax,-0x24(%rbp)
mov    -0x24(%rbp),%eax
mov    -0x28(%rbp),%ecx
add    $0x1,%ecx
shl    $0x6,%ecx
cmp    %ecx,%eax
jge    1478 <Edit_Distance_multiple_word_NoEndPenaltySeq1+0x348>
mov    -0x24(%rbp),%eax
cmp    -0x1c(%rbp),%eax
jg     1465 <Edit_Distance_multiple_word_NoEndPenaltySeq1+0x335>
cmpl   $0x0,-0x24(%rbp)
jne    132f <Edit_Distance_multiple_word_NoEndPenaltySeq1+0x1ff>
cmpl   $0x0,-0x28(%rbp)
je     1459 <Edit_Distance_multiple_word_NoEndPenaltySeq1+0x329>
mov    -0x10(%rbp),%rax
mov    -0x24(%rbp),%ecx
add    $0xffffffff,%ecx
movslq %ecx,%rcx
movsbl (%rax,%rcx,1),%eax
add    $0xffffffbf,%eax
mov    %eax,%ecx
mov    %rcx,-0x130(%rbp)
sub    $0x13,%eax
ja     13e9 <Edit_Distance_multiple_word_NoEndPenaltySeq1+0x2b9>
mov    -0x130(%rbp),%rax
lea    0xced(%rip),%rcx
movslq (%rcx,%rax,4),%rax
add    %rcx,%rax
jmp    *%rax
mov    -0x60(%rbp),%rdx
mov    -0x30(%rbp),%rax
movslq -0x28(%rbp),%rcx
or     (%rax,%rcx,8),%rdx
mov    %rdx,(%rax,%rcx,8)
jmp    1454 <Edit_Distance_multiple_word_NoEndPenaltySeq1+0x324>
mov    -0x60(%rbp),%rdx
mov    -0x38(%rbp),%rax
movslq -0x28(%rbp),%rcx
or     (%rax,%rcx,8),%rdx
mov    %rdx,(%rax,%rcx,8)
jmp    1454 <Edit_Distance_multiple_word_NoEndPenaltySeq1+0x324>
mov    -0x60(%rbp),%rdx
mov    -0x40(%rbp),%rax
movslq -0x28(%rbp),%rcx
or     (%rax,%rcx,8),%rdx
mov    %rdx,(%rax,%rcx,8)
jmp    1454 <Edit_Distance_multiple_word_NoEndPenaltySeq1+0x324>
mov    -0x60(%rbp),%rdx
mov    -0x48(%rbp),%rax
movslq -0x28(%rbp),%rcx
or     (%rax,%rcx,8),%rdx
mov    %rdx,(%rax,%rcx,8)
jmp    1454 <Edit_Distance_multiple_word_NoEndPenaltySeq1+0x324>
mov    -0x60(%rbp),%rdx
mov    -0x50(%rbp),%rax
movslq -0x28(%rbp),%rcx
or     (%rax,%rcx,8),%rdx
mov    %rdx,(%rax,%rcx,8)
jmp    1454 <Edit_Distance_multiple_word_NoEndPenaltySeq1+0x324>
mov    -0x24(%rbp),%eax
mov    -0x10(%rbp),%rcx
movslq -0x24(%rbp),%rdx
movsbl (%rcx,%rdx,1),%edx
lea    0xca1(%rip),%rdi
movsbl %al,%esi
mov    $0x0,%al
call   1040 <printf@plt>
mov    -0x30(%rbp),%rdi
call   1030 <free@plt>
mov    -0x38(%rbp),%rdi
call   1030 <free@plt>
mov    -0x40(%rbp),%rdi
call   1030 <free@plt>
mov    -0x48(%rbp),%rdi
call   1030 <free@plt>
mov    -0x50(%rbp),%rdi
call   1030 <free@plt>
mov    -0x70(%rbp),%rdi
call   1030 <free@plt>
mov    -0x78(%rbp),%rdi
call   1030 <free@plt>
movl   $0xffffffff,-0x4(%rbp)
jmp    190b <Edit_Distance_multiple_word_NoEndPenaltySeq1+0x7db>
jmp    1459 <Edit_Distance_multiple_word_NoEndPenaltySeq1+0x329>
mov    -0x60(%rbp),%rax
shl    $0x1,%rax
mov    %rax,-0x60(%rbp)
jmp    146a <Edit_Distance_multiple_word_NoEndPenaltySeq1+0x33a>
mov    -0x24(%rbp),%eax
add    $0x1,%eax
mov    %eax,-0x24(%rbp)
jmp    12fb <Edit_Distance_multiple_word_NoEndPenaltySeq1+0x1cb>
jmp    147d <Edit_Distance_multiple_word_NoEndPenaltySeq1+0x34d>
mov    -0x28(%rbp),%eax
add    $0x1,%eax
mov    %eax,-0x28(%rbp)
jmp    128b <Edit_Distance_multiple_word_NoEndPenaltySeq1+0x15b>
mov    -0x70(%rbp),%rax
movq   $0x1,(%rax)
mov    -0x78(%rbp),%rax
movq   $0x1,(%rax)
movl   $0x0,-0x24(%rbp)
mov    -0x24(%rbp),%eax
cmp    -0x20(%rbp),%eax
jge    179c <Edit_Distance_multiple_word_NoEndPenaltySeq1+0x66c>
movq   $0x0,-0xd8(%rbp)
movq   $0x1,-0xe0(%rbp)
movq   $0x0,-0xe8(%rbp)
mov    -0x18(%rbp),%rax
movslq -0x24(%rbp),%rcx
movsbl (%rax,%rcx,1),%eax
add    $0xffffffbf,%eax
mov    %eax,%ecx
mov    %rcx,-0x138(%rbp)
sub    $0x13,%eax
ja     154e <Edit_Distance_multiple_word_NoEndPenaltySeq1+0x41e>
mov    -0x138(%rbp),%rax
lea    0xafc(%rip),%rcx
movslq (%rcx,%rax,4),%rax
add    %rcx,%rax
jmp    *%rax
mov    -0x30(%rbp),%rax
mov    %rax,-0x58(%rbp)
jmp    15b3 <Edit_Distance_multiple_word_NoEndPenaltySeq1+0x483>
mov    -0x38(%rbp),%rax
mov    %rax,-0x58(%rbp)
jmp    15b3 <Edit_Distance_multiple_word_NoEndPenaltySeq1+0x483>
mov    -0x40(%rbp),%rax
mov    %rax,-0x58(%rbp)
jmp    15b3 <Edit_Distance_multiple_word_NoEndPenaltySeq1+0x483>
mov    -0x48(%rbp),%rax
mov    %rax,-0x58(%rbp)
jmp    15b3 <Edit_Distance_multiple_word_NoEndPenaltySeq1+0x483>
mov    -0x50(%rbp),%rax
mov    %rax,-0x58(%rbp)
jmp    15b3 <Edit_Distance_multiple_word_NoEndPenaltySeq1+0x483>
mov    -0x18(%rbp),%rax
movslq -0x24(%rbp),%rcx
lea    0xb80(%rip),%rdi
movsbl (%rax,%rcx,1),%esi
mov    $0x0,%al
call   1040 <printf@plt>
mov    -0x30(%rbp),%rdi
call   1030 <free@plt>
mov    -0x38(%rbp),%rdi
call   1030 <free@plt>
mov    -0x40(%rbp),%rdi
call   1030 <free@plt>
mov    -0x48(%rbp),%rdi
call   1030 <free@plt>
mov    -0x50(%rbp),%rdi
call   1030 <free@plt>
mov    -0x70(%rbp),%rdi
call   1030 <free@plt>
mov    -0x78(%rbp),%rdi
call   1030 <free@plt>
movl   $0xffffffff,-0x4(%rbp)
jmp    190b <Edit_Distance_multiple_word_NoEndPenaltySeq1+0x7db>
movl   $0x0,-0x28(%rbp)
mov    -0x28(%rbp),%eax
cmp    -0x124(%rbp),%eax
jge    1789 <Edit_Distance_multiple_word_NoEndPenaltySeq1+0x659>
mov    -0xe0(%rbp),%rax
mov    %rax,-0xf0(%rbp)
mov    -0xe8(%rbp),%rax
mov    %rax,-0xf8(%rbp)
mov    -0x58(%rbp),%rax
movslq -0x28(%rbp),%rcx
mov    (%rax,%rcx,8),%rax
mov    %rax,-0x68(%rbp)
mov    -0x68(%rbp),%rax
mov    -0x70(%rbp),%rcx
movslq -0x28(%rbp),%rdx
or     (%rcx,%rdx,8),%rax
mov    %rax,-0x80(%rbp)
mov    -0x80(%rbp),%rax
xor    $0xffffffffffffffff,%rax
mov    %rax,-0x88(%rbp)
mov    -0x88(%rbp),%rax
mov    -0x78(%rbp),%rcx
movslq -0x28(%rbp),%rdx
or     (%rcx,%rdx,8),%rax
mov    %rax,-0x90(%rbp)
mov    -0x90(%rbp),%rax
mov    -0x70(%rbp),%rcx
movslq -0x28(%rbp),%rdx
xor    (%rcx,%rdx,8),%rax
mov    %rax,-0x98(%rbp)
mov    -0x90(%rbp),%rax
mov    -0x78(%rbp),%rcx
movslq -0x28(%rbp),%rdx
add    (%rcx,%rdx,8),%rax
add    -0xd8(%rbp),%rax
mov    %rax,-0xc0(%rbp)
mov    -0xc0(%rbp),%rax
cmp    -0x90(%rbp),%rax
jae    168c <Edit_Distance_multiple_word_NoEndPenaltySeq1+0x55c>
movq   $0x1,-0xd8(%rbp)
mov    -0xc0(%rbp),%rax
and    -0x88(%rbp),%rax
mov    %rax,-0xc8(%rbp)
mov    -0xc8(%rbp),%rax
xor    -0x98(%rbp),%rax
mov    %rax,-0xa0(%rbp)
mov    -0x70(%rbp),%rax
movslq -0x28(%rbp),%rcx
mov    (%rax,%rcx,8),%rax
mov    -0xc8(%rbp),%rcx
mov    -0x78(%rbp),%rdx
movslq -0x28(%rbp),%rsi
and    (%rdx,%rsi,8),%rcx
or     %rcx,%rax
mov    %rax,-0xa8(%rbp)
mov    -0xa0(%rbp),%rax
and    -0xd0(%rbp),%rax
shr    $0x3f,%rax
mov    %rax,-0xe8(%rbp)
mov    -0xa8(%rbp),%rax
and    -0xd0(%rbp),%rax
shr    $0x3f,%rax
mov    %rax,-0xe0(%rbp)
mov    -0xa0(%rbp),%rax
shl    $0x1,%rax
add    -0xf8(%rbp),%rax
mov    %rax,-0xb0(%rbp)
mov    -0xa8(%rbp),%rax
shl    $0x1,%rax
add    -0xf0(%rbp),%rax
mov    %rax,-0xb8(%rbp)
mov    -0x80(%rbp),%rdx
and    -0xb8(%rbp),%rdx
mov    -0x70(%rbp),%rax
movslq -0x28(%rbp),%rcx
mov    %rdx,(%rax,%rcx,8)
mov    -0xb8(%rbp),%rdx
mov    -0x80(%rbp),%rax
and    -0xb0(%rbp),%rax
or     %rax,%rdx
mov    -0x78(%rbp),%rax
movslq -0x28(%rbp),%rcx
mov    %rdx,(%rax,%rcx,8)
mov    -0x28(%rbp),%eax
add    $0x1,%eax
mov    %eax,-0x28(%rbp)
jmp    15ba <Edit_Distance_multiple_word_NoEndPenaltySeq1+0x48a>
jmp    178e <Edit_Distance_multiple_word_NoEndPenaltySeq1+0x65e>
mov    -0x24(%rbp),%eax
add    $0x1,%eax
mov    %eax,-0x24(%rbp)
jmp    14a8 <Edit_Distance_multiple_word_NoEndPenaltySeq1+0x378>
movq   $0x1,-0x110(%rbp)
mov    -0x20(%rbp),%eax
mov    %eax,-0x118(%rbp)
mov    -0x20(%rbp),%eax
mov    %eax,-0x114(%rbp)
movl   $0x0,-0x28(%rbp)
mov    -0x28(%rbp),%eax
cmp    -0x124(%rbp),%eax
jge    18c3 <Edit_Distance_multiple_word_NoEndPenaltySeq1+0x793>
mov    -0x70(%rbp),%rax
movslq -0x28(%rbp),%rcx
mov    (%rax,%rcx,8),%rax
mov    %rax,-0x100(%rbp)
mov    -0x78(%rbp),%rax
movslq -0x28(%rbp),%rcx
mov    (%rax,%rcx,8),%rax
xor    $0xffffffffffffffff,%rax
mov    %rax,-0x108(%rbp)
movl   $0x0,-0x24(%rbp)
cmpl   $0x40,-0x24(%rbp)
jge    18b0 <Edit_Distance_multiple_word_NoEndPenaltySeq1+0x780>
mov    -0x24(%rbp),%eax
or     -0x28(%rbp),%eax
cmp    $0x0,%eax
je     187e <Edit_Distance_multiple_word_NoEndPenaltySeq1+0x74e>
mov    -0x100(%rbp),%rax
movslq %eax,%rcx
and    -0x110(%rbp),%rcx
movslq -0x114(%rbp),%rax
sub    %rcx,%rax
mov    %eax,-0x114(%rbp)
mov    -0x108(%rbp),%rax
movslq %eax,%rcx
and    -0x110(%rbp),%rcx
movslq -0x114(%rbp),%rax
add    %rcx,%rax
mov    %eax,-0x114(%rbp)
mov    -0x114(%rbp),%eax
cmp    -0x118(%rbp),%eax
jge    1879 <Edit_Distance_multiple_word_NoEndPenaltySeq1+0x749>
mov    -0x114(%rbp),%eax
mov    %eax,-0x118(%rbp)
jmp    187e <Edit_Distance_multiple_word_NoEndPenaltySeq1+0x74e>
mov    -0x100(%rbp),%rax
shr    $0x1,%rax
mov    %rax,-0x100(%rbp)
mov    -0x108(%rbp),%rax
shr    $0x1,%rax
mov    %rax,-0x108(%rbp)
mov    -0x24(%rbp),%eax
add    $0x1,%eax
mov    %eax,-0x24(%rbp)
jmp    1800 <Edit_Distance_multiple_word_NoEndPenaltySeq1+0x6d0>
jmp    18b5 <Edit_Distance_multiple_word_NoEndPenaltySeq1+0x785>
mov    -0x28(%rbp),%eax
add    $0x1,%eax
mov    %eax,-0x28(%rbp)
jmp    17c0 <Edit_Distance_multiple_word_NoEndPenaltySeq1+0x690>
mov    -0x30(%rbp),%rdi
call   1030 <free@plt>
mov    -0x38(%rbp),%rdi
call   1030 <free@plt>
mov    -0x40(%rbp),%rdi
call   1030 <free@plt>
mov    -0x48(%rbp),%rdi
call   1030 <free@plt>
mov    -0x50(%rbp),%rdi
call   1030 <free@plt>
mov    -0x70(%rbp),%rdi
call   1030 <free@plt>
mov    -0x78(%rbp),%rdi
call   1030 <free@plt>
mov    -0x118(%rbp),%eax
mov    %eax,-0x4(%rbp)
mov    -0x4(%rbp),%eax
add    $0x140,%rsp
pop    %rbp
ret

x86 assembly (clang, -O2):
<Edit_Distance_multiple_word_NoEndPenaltySeq1>:
push   %rbp
push   %r15
push   %r14
push   %r13
push   %r12
push   %rbx
sub    $0x68,%rsp
mov    %rsi,0x48(%rsp)
mov    %rdi,0x20(%rsp)
test   %ecx,%ecx
je     1381 <Edit_Distance_multiple_word_NoEndPenaltySeq1+0x251>
mov    %ecx,%ebx
mov    %edx,%ebp
mov    $0x1,%r12d
cmp    $0x40,%edx
jl     117f <Edit_Distance_multiple_word_NoEndPenaltySeq1+0x4f>
lea    -0x3f(%rbp),%eax
mov    %eax,%ecx
shr    $0x6,%ecx
mov    %ecx,%edx
shl    $0x6,%edx
sub    %edx,%eax
xor    %edx,%edx
test   %eax,%eax
setle  %dl
neg    %edx
lea    (%rcx,%rdx,1),%r12d
add    $0x2,%r12d
mov    %r12d,%edi
mov    $0x8,%esi
call   1050 <calloc@plt>
mov    %rax,0x18(%rsp)
mov    %r12d,%edi
mov    $0x8,%esi
call   1050 <calloc@plt>
mov    %rax,(%rsp)
mov    %r12d,%edi
mov    $0x8,%esi
call   1050 <calloc@plt>
mov    %rax,0x8(%rsp)
mov    %r12d,%edi
mov    $0x8,%esi
call   1050 <calloc@plt>
mov    %rax,0x10(%rsp)
mov    %r12d,%edi
mov    $0x8,%esi
call   1050 <calloc@plt>
mov    %rax,%r14
mov    %r12d,%edi
mov    $0x8,%esi
call   1050 <calloc@plt>
mov    %rax,0x30(%rsp)
mov    %r12d,%edi
mov    $0x8,%esi
call   1050 <calloc@plt>
mov    %rax,%r9
movslq %ebp,%rcx
mov    %r12d,%r10d
xor    %r15d,%r15d
lea    0xdf8(%rip),%rdx
xor    %r12d,%r12d
mov    %r10,0x38(%rsp)
jmp    1232 <Edit_Distance_multiple_word_NoEndPenaltySeq1+0x102>
cs nopw 0x0(%rax,%rax,1)
nopl   0x0(%rax)
add    $0x40,%r12d
mov    0x38(%rsp),%r10
cmp    %r10,%r15
je     1388 <Edit_Distance_multiple_word_NoEndPenaltySeq1+0x258>
mov    %r12d,%eax
mov    %r15,%rbp
movslq %r12d,%rdi
mov    %r12d,%r12d
mov    0x18(%rsp),%rax
lea    (%rax,%r15,8),%r8
movq   $0x0,(%rax,%r15,8)
mov    (%rsp),%rax
lea    (%rax,%r15,8),%rsi
mov    %rsi,0x28(%rsp)
movq   $0x0,(%rax,%r15,8)
mov    0x8(%rsp),%rax
lea    (%rax,%r15,8),%rsi
mov    %rsi,0x60(%rsp)
movq   $0x0,(%rax,%r15,8)
mov    0x10(%rsp),%rax
lea    (%rax,%r15,8),%rsi
mov    %rsi,0x58(%rsp)
movq   $0x0,(%rax,%r15,8)
lea    (%r14,%r15,8),%rax
mov    %rax,0x50(%rsp)
movq   $0x0,(%r14,%r15,8)
add    $0x1,%r15
mov    %r15d,%r11d
shl    $0x6,%r11d
mov    $0x1,%r10d
mov    %r12,%rsi
jmp    12d7 <Edit_Distance_multiple_word_NoEndPenaltySeq1+0x1a7>
mov    0x28(%rsp),%rax
nopl   0x0(%rax)
or     %r10,(%rax)
add    %r10,%r10
add    $0x1,%rdi
add    $0x1,%rsi
cmp    %esi,%r11d
jbe    1220 <Edit_Distance_multiple_word_NoEndPenaltySeq1+0xf0>
cmp    %rcx,%rdi
jg     12c6 <Edit_Distance_multiple_word_NoEndPenaltySeq1+0x196>
mov    %rdi,%rax
or     %rbp,%rax
je     12c3 <Edit_Distance_multiple_word_NoEndPenaltySeq1+0x193>
mov    0x20(%rsp),%rax
movsbl -0x1(%rax,%rdi,1),%eax
add    $0xffffffbf,%eax
cmp    $0x13,%eax
ja     1318 <Edit_Distance_multiple_word_NoEndPenaltySeq1+0x1e8>
movslq (%rdx,%rax,4),%r13
add    %rdx,%r13
mov    %r8,%rax
jmp    *%r13
mov    0x60(%rsp),%rax
jmp    12c0 <Edit_Distance_multiple_word_NoEndPenaltySeq1+0x190>
mov    0x50(%rsp),%rax
jmp    12c0 <Edit_Distance_multiple_word_NoEndPenaltySeq1+0x190>
mov    0x58(%rsp),%rax
jmp    12c0 <Edit_Distance_multiple_word_NoEndPenaltySeq1+0x190>
mov    0x20(%rsp),%rax
movsbl (%rax,%rsi,1),%edx
movsbl %dil,%esi
lea    0xd74(%rip),%rdi
xor    %eax,%eax
mov    %r9,%rbx
call   1040 <printf@plt>
mov    0x18(%rsp),%rdi
call   1030 <free@plt>
mov    (%rsp),%rdi
call   1030 <free@plt>
mov    0x8(%rsp),%rdi
call   1030 <free@plt>
mov    0x10(%rsp),%rdi
call   1030 <free@plt>
mov    %r14,%rdi
call   1030 <free@plt>
mov    0x30(%rsp),%rdi
call   1030 <free@plt>
mov    %rbx,%rdi
call   1030 <free@plt>
mov    $0xffffffff,%ebx
jmp    1587 <Edit_Distance_multiple_word_NoEndPenaltySeq1+0x457>
xor    %ebx,%ebx
jmp    1587 <Edit_Distance_multiple_word_NoEndPenaltySeq1+0x457>
mov    0x30(%rsp),%r12
movq   $0x1,(%r12)
movq   $0x1,(%r9)
test   %ebx,%ebx
jle    14d0 <Edit_Distance_multiple_word_NoEndPenaltySeq1+0x3a0>
mov    %ebx,%eax
mov    %rax,0x28(%rsp)
xor    %edx,%edx
mov    %r14,0x40(%rsp)
mov    $0x1,%r15d
nopl   0x0(%rax,%rax,1)
mov    0x48(%rsp),%rax
movsbl (%rax,%rdx,1),%eax
lea    -0x41(%rax),%ecx
cmp    $0x13,%ecx
ja     1598 <Edit_Distance_multiple_word_NoEndPenaltySeq1+0x468>
lea    0xc74(%rip),%rsi
movslq (%rsi,%rcx,4),%rcx
add    %rsi,%rcx
mov    0x18(%rsp),%r13
jmp    *%rcx
mov    (%rsp),%r13
jmp    1410 <Edit_Distance_multiple_word_NoEndPenaltySeq1+0x2e0>
mov    0x8(%rsp),%r13
jmp    1410 <Edit_Distance_multiple_word_NoEndPenaltySeq1+0x2e0>
mov    %r14,%r13
jmp    1410 <Edit_Distance_multiple_word_NoEndPenaltySeq1+0x2e0>
mov    0x10(%rsp),%r13
cs nopw 0x0(%rax,%rax,1)
nopl   0x0(%rax,%rax,1)
mov    %rdx,0x20(%rsp)
mov    $0x1,%r14d
xor    %ebp,%ebp
xor    %edx,%edx
xor    %ecx,%ecx
cs nopw 0x0(%rax,%rax,1)
nopl   0x0(%rax,%rax,1)
mov    (%r12,%rbp,8),%r10
mov    0x0(%r13,%rbp,8),%r11
or     %r10,%r11
mov    %r11,%rdi
not    %rdi
mov    %r9,%rsi
mov    (%r9,%rbp,8),%r9
mov    %r9,%rax
or     %rdi,%rax
mov    %rax,%r8
xor    %r10,%r8
lea    (%r9,%rcx,1),%r12
add    %r12,%rax
mov    0x30(%rsp),%r12
cmovb  %r15,%rcx
and    %rdi,%rax
xor    %rax,%r8
and    %r9,%rax
mov    %rsi,%r9
or     %r10,%rax
mov    0x38(%rsp),%r10
mov    %r8,%rdi
add    %r8,%r8
or     %rdx,%r8
mov    %rax,%rsi
add    %rax,%rax
or     %r14,%rax
and    %r11,%r8
or     %rax,%r8
and    %r11,%rax
mov    %rax,(%r12,%rbp,8)
mov    %r8,(%r9,%rbp,8)
shr    $0x3f,%rdi
shr    $0x3f,%rsi
add    $0x1,%rbp
mov    %rdi,%rdx
mov    %rsi,%r14
cmp    %rbp,%r10
jne    1430 <Edit_Distance_multiple_word_NoEndPenaltySeq1+0x300>
mov    0x20(%rsp),%rdx
add    $0x1,%rdx
cmp    0x28(%rsp),%rdx
mov    0x40(%rsp),%r14
jne    13c0 <Edit_Distance_multiple_word_NoEndPenaltySeq1+0x290>
xor    %r8d,%r8d
mov    %ebx,%edx
jmp    14e9 <Edit_Distance_multiple_word_NoEndPenaltySeq1+0x3b9>
nopw   0x0(%rax,%rax,1)
add    $0x1,%r8
cmp    %r10,%r8
je     1545 <Edit_Distance_multiple_word_NoEndPenaltySeq1+0x415>
mov    (%r12,%r8,8),%rax
mov    (%r9,%r8,8),%rsi
not    %rsi
xor    %ebp,%ebp
jmp    1529 <Edit_Distance_multiple_word_NoEndPenaltySeq1+0x3f9>
nopl   0x0(%rax,%rax,1)
mov    %eax,%edi
shr    %edi
and    $0x1,%edi
mov    %edx,%ecx
sub    %edi,%ecx
mov    %esi,%edx
shr    %edx
and    $0x1,%edx
add    %ecx,%edx
cmp    %ebx,%edx
cmovl  %edx,%ebx
shr    $0x2,%rax
shr    $0x2,%rsi
add    $0x2,%ebp
cmp    $0x40,%ebp
je     14e0 <Edit_Distance_multiple_word_NoEndPenaltySeq1+0x3b0>
mov    %ebp,%edi
or     %r8d,%edi
je     1500 <Edit_Distance_multiple_word_NoEndPenaltySeq1+0x3d0>
mov    %eax,%edi
and    $0x1,%edi
sub    %edi,%edx
mov    %esi,%edi
and    $0x1,%edi
add    %edi,%edx
cmp    %ebx,%edx
cmovl  %edx,%ebx
jmp    1500 <Edit_Distance_multiple_word_NoEndPenaltySeq1+0x3d0>
mov    0x18(%rsp),%rdi
mov    %r9,%rbp
call   1030 <free@plt>
mov    (%rsp),%rdi
call   1030 <free@plt>
mov    0x8(%rsp),%rdi
call   1030 <free@plt>
mov    0x10(%rsp),%rdi
call   1030 <free@plt>
mov    %r14,%rdi
call   1030 <free@plt>
mov    %r12,%rdi
call   1030 <free@plt>
mov    %rbp,%rdi
call   1030 <free@plt>
mov    %ebx,%eax
add    $0x68,%rsp
pop    %rbx
pop    %r12
pop    %r13
pop    %r14
pop    %r15
pop    %rbp
ret
movsbl %al,%esi
lea    0xb3b(%rip),%rdi
xor    %eax,%eax
mov    %r9,%rbx
call   1040 <printf@plt>
mov    0x18(%rsp),%rdi
call   1030 <free@plt>
mov    (%rsp),%rdi
call   1030 <free@plt>
mov    0x8(%rsp),%rdi
call   1030 <free@plt>
mov    0x10(%rsp),%rdi
call   1030 <free@plt>
mov    %r14,%rdi
call   1030 <free@plt>
mov    %r12,%rdi
jmp    136a <Edit_Distance_multiple_word_NoEndPenaltySeq1+0x23a>

LLVM IR (-O0):
@.str = [61 x i8] c"\0AError, non-ACGTN character read at position %d in string:%c\00"
@.str.1 = [46 x i8] c"\0AError, non-ACGTN character read in string:%c\00"
define i32 @Edit_Distance_multiple_word_NoEndPenaltySeq1(i8* %0, i8* %1, i32 %2, i32 %3) {
%5 = alloca i32
%6 = alloca i8*
%7 = alloca i8*
%8 = alloca i32
%9 = alloca i32
%10 = alloca i32
%11 = alloca i32
%12 = alloca i64*
%13 = alloca i64*
%14 = alloca i64*
%15 = alloca i64*
%16 = alloca i64*
%17 = alloca i64*
%18 = alloca i64
%19 = alloca i64
%20 = alloca i64*
%21 = alloca i64*
%22 = alloca i64
%23 = alloca i64
%24 = alloca i64
%25 = alloca i64
%26 = alloca i64
%27 = alloca i64
%28 = alloca i64
%29 = alloca i64
%30 = alloca i64
%31 = alloca i64
%32 = alloca i64
%33 = alloca i64
%34 = alloca i64
%35 = alloca i64
%36 = alloca i64
%37 = alloca i64
%38 = alloca i64
%39 = alloca i64
%40 = alloca i64
%41 = alloca i32
%42 = alloca i32
%43 = alloca i32
%44 = alloca i32
%45 = alloca i32
store i8* %0, i8** %6
store i8* %1, i8** %7
store i32 %2, i32* %8
store i32 %3, i32* %9
store i64 -9223372036854775808, i64* %32
%46 = load i32, i32* %9
%47 = icmp eq i32 %46, 0
br i1 %47, label %48, label %49
48: ; preds = %4
store i32 0, i32* %5
br label %458
49: ; preds = %4
%50 = load i32, i32* %8
%51 = icmp sgt i32 %50, 63
br i1 %51, label %52, label %72
52: ; preds = %49
%53 = load i32, i32* %8
%54 = sub nsw i32 %53, 64
%55 = add nsw i32 %54, 1
%56 = sdiv i32 %55, 64
store i32 %56, i32* %44
%57 = load i32, i32* %8
%58 = sub nsw i32 %57, 64
%59 = add nsw i32 %58, 1
%60 = load i32, i32* %44
%61 = mul nsw i32 64, %60
%62 = sub nsw i32 %59, %61
%63 = icmp sgt i32 %62, 0
br i1 %63, label %64, label %67
64: ; preds = %52
%65 = load i32, i32* %44
%66 = add nsw i32 %65, 2
br label %70
67: ; preds = %52
%68 = load i32, i32* %44
%69 = add nsw i32 %68, 1
br label %70
70: ; preds = %67, %64
%71 = phi i32 [ %66, %64 ], [ %69, %67 ]
store i32 %71, i32* %43
br label %73
72: ; preds = %49
store i32 1, i32* %43
br label %73
73: ; preds = %72, %70
%74 = load i32, i32* %43
store i32 %74, i32* %45
%75 = load i32, i32* %45
%76 = call i64 @calloc(i32 %75, i32 8)
%77 = inttoptr i64 %76 to i64*
store i64* %77, i64** %12
%78 = load i32, i32* %45
%79 = call i64 @calloc(i32 %78, i32 8)
%80 = inttoptr i64 %79 to i64*
store i64* %80, i64** %13
%81 = load i32, i32* %45
%82 = call i64 @calloc(i32 %81, i32 8)
%83 = inttoptr i64 %82 to i64*
store i64* %83, i64** %14
%84 = load i32, i32* %45
%85 = call i64 @calloc(i32 %84, i32 8)
%86 = inttoptr i64 %85 to i64*
store i64* %86, i64** %15
%87 = load i32, i32* %45
%88 = call i64 @calloc(i32 %87, i32 8)
%89 = inttoptr i64 %88 to i64*
store i64* %89, i64** %16
%90 = load i32, i32* %45
%91 = call i64 @calloc(i32 %90, i32 8)
%92 = inttoptr i64 %91 to i64*
store i64* %92, i64** %20
%93 = load i32, i32* %45
%94 = call i64 @calloc(i32 %93, i32 8)
%95 = inttoptr i64 %94 to i64*
store i64* %95, i64** %21
store i32 0, i32* %11
br label %96
96: ; preds = %220, %73
%97 = load i32, i32* %11
%98 = load i32, i32* %45
%99 = icmp slt i32 %97, %98
br i1 %99, label %100, label %223
100: ; preds = %96
store i64 1, i64* %18
%101 = load i64*, i64** %12
%102 = load i32, i32* %11
%103 = sext i32 %102 to i64
%104 = getelementptr inbounds i64, i64* %101, i64 %103
store i64 0, i64* %104
%105 = load i64*, i64** %13
%106 = load i32, i32* %11
%107 = sext i32 %106 to i64
%108 = getelementptr inbounds i64, i64* %105, i64 %107
store i64 0, i64* %108
%109 = load i64*, i64** %14
%110 = load i32, i32* %11
%111 = sext i32 %110 to i64
%112 = getelementptr inbounds i64, i64* %109, i64 %111
store i64 0, i64* %112
%113 = load i64*, i64** %15
%114 = load i32, i32* %11
%115 = sext i32 %114 to i64
%116 = getelementptr inbounds i64, i64* %113, i64 %115
store i64 0, i64* %116
%117 = load i64*, i64** %16
%118 = load i32, i32* %11
%119 = sext i32 %118 to i64
%120 = getelementptr inbounds i64, i64* %117, i64 %119
store i64 0, i64* %120
%121 = load i32, i32* %11
%122 = mul nsw i32 %121, 64
store i32 %122, i32* %10
br label %123
123: ; preds = %216, %100
%124 = load i32, i32* %10
%125 = load i32, i32* %11
%126 = add nsw i32 %125, 1
%127 = mul nsw i32 %126, 64
%128 = icmp slt i32 %124, %127
br i1 %128, label %129, label %219
129: ; preds = %123
%130 = load i32, i32* %10
%131 = load i32, i32* %8
%132 = icmp sle i32 %130, %131
br i1 %132, label %133, label %215
133: ; preds = %129
%134 = load i32, i32* %10
%135 = icmp ne i32 %134, 0
br i1 %135, label %139, label %136
136: ; preds = %133
%137 = load i32, i32* %11
%138 = icmp ne i32 %137, 0
br i1 %138, label %139, label %212
139: ; preds = %136, %133
%140 = load i8*, i8** %6
%141 = load i32, i32* %10
%142 = sub nsw i32 %141, 1
%143 = sext i32 %142 to i64
%144 = getelementptr inbounds i8, i8* %140, i64 %143
%145 = load i8, i8* %144
%146 = sext i8 %145 to i32
switch i32 %146, label %187 [
i32 65, label %147
i32 67, label %155
i32 71, label %163
i32 84, label %171
i32 78, label %179
]
147: ; preds = %139
%148 = load i64, i64* %18
%149 = load i64*, i64** %12
%150 = load i32, i32* %11
%151 = sext i32 %150 to i64
%152 = getelementptr inbounds i64, i64* %149, i64 %151
%153 = load i64, i64* %152
%154 = or i64 %153, %148
store i64 %154, i64* %152
br label %211
155: ; preds = %139
%156 = load i64, i64* %18
%157 = load i64*, i64** %13
%158 = load i32, i32* %11
%159 = sext i32 %158 to i64
%160 = getelementptr inbounds i64, i64* %157, i64 %159
%161 = load i64, i64* %160
%162 = or i64 %161, %156
store i64 %162, i64* %160
br label %211
163: ; preds = %139
%164 = load i64, i64* %18
%165 = load i64*, i64** %14
%166 = load i32, i32* %11
%167 = sext i32 %166 to i64
%168 = getelementptr inbounds i64, i64* %165, i64 %167
%169 = load i64, i64* %168
%170 = or i64 %169, %164
store i64 %170, i64* %168
br label %211
171: ; preds = %139
%172 = load i64, i64* %18
%173 = load i64*, i64** %15
%174 = load i32, i32* %11
%175 = sext i32 %174 to i64
%176 = getelementptr inbounds i64, i64* %173, i64 %175
%177 = load i64, i64* %176
%178 = or i64 %177, %172
store i64 %178, i64* %176
br label %211
179: ; preds = %139
%180 = load i64, i64* %18
%181 = load i64*, i64** %16
%182 = load i32, i32* %11
%183 = sext i32 %182 to i64
%184 = getelementptr inbounds i64, i64* %181, i64 %183
%185 = load i64, i64* %184
%186 = or i64 %185, %180
store i64 %186, i64* %184
br label %211
187: ; preds = %139
%188 = load i32, i32* %10
%189 = trunc i32 %188 to i8
%190 = load i8*, i8** %6
%191 = load i32, i32* %10
%192 = sext i32 %191 to i64
%193 = getelementptr inbounds i8, i8* %190, i64 %192
%194 = load i8, i8* %193
%195 = sext i8 %194 to i32
%196 = call i32 (i8*, i8, ...) @printf(i8* getelementptr inbounds ([61 x i8], [61 x i8]* @.str, i64 0, i64 0), i8 signext %189, i32 %195)
%197 = load i64*, i64** %12
%198 = call i32 @free(i64* %197)
%199 = load i64*, i64** %13
%200 = call i32 @free(i64* %199)
%201 = load i64*, i64** %14
%202 = call i32 @free(i64* %201)
%203 = load i64*, i64** %15
%204 = call i32 @free(i64* %203)
%205 = load i64*, i64** %16
%206 = call i32 @free(i64* %205)
%207 = load i64*, i64** %20
%208 = call i32 @free(i64* %207)
%209 = load i64*, i64** %21
%210 = call i32 @free(i64* %209)
store i32 -1, i32* %5
br label %458
211: ; preds = %179, %171, %163, %155, %147
br label %212
212: ; preds = %211, %136
%213 = load i64, i64* %18
%214 = shl i64 %213, 1
store i64 %214, i64* %18
br label %215
215: ; preds = %212, %129
br label %216
216: ; preds = %215
%217 = load i32, i32* %10
%218 = add nsw i32 %217, 1
store i32 %218, i32* %10
br label %123
219: ; preds = %123
br label %220
220: ; preds = %219
%221 = load i32, i32* %11
%222 = add nsw i32 %221, 1
store i32 %222, i32* %11
br label %96
223: ; preds = %96
%224 = load i64*, i64** %20
%225 = getelementptr inbounds i64, i64* %224, i64 0
store i64 1, i64* %225
%226 = load i64*, i64** %21
%227 = getelementptr inbounds i64, i64* %226, i64 0
store i64 1, i64* %227
store i32 0, i32* %10
br label %228
228: ; preds = %375, %223
%229 = load i32, i32* %10
%230 = load i32, i32* %9
%231 = icmp slt i32 %229, %230
br i1 %231, label %232, label %378
232: ; preds = %228
store i64 0, i64* %33
store i64 1, i64* %34
store i64 0, i64* %35
%233 = load i8*, i8** %7
%234 = load i32, i32* %10
%235 = sext i32 %234 to i64
%236 = getelementptr inbounds i8, i8* %233, i64 %235
%237 = load i8, i8* %236
%238 = sext i8 %237 to i32
switch i32 %238, label %249 [
i32 65, label %239
i32 67, label %241
i32 71, label %243
i32 84, label %245
i32 78, label %247
]
239: ; preds = %232
%240 = load i64*, i64** %12
store i64* %240, i64** %17
br label %270
241: ; preds = %232
%242 = load i64*, i64** %13
store i64* %242, i64** %17
br label %270
243: ; preds = %232
%244 = load i64*, i64** %14
store i64* %244, i64** %17
br label %270
245: ; preds = %232
%246 = load i64*, i64** %15
store i64* %246, i64** %17
br label %270
247: ; preds = %232
%248 = load i64*, i64** %16
store i64* %248, i64** %17
br label %270
249: ; preds = %232
%250 = load i8*, i8** %7
%251 = load i32, i32* %10
%252 = sext i32 %251 to i64
%253 = getelementptr inbounds i8, i8* %250, i64 %252
%254 = load i8, i8* %253
%255 = call i32 (i8*, i8, ...) @printf(i8* getelementptr inbounds ([46 x i8], [46 x i8]* @.str.1, i64 0, i64 0), i8 signext %254)
%256 = load i64*, i64** %12
%257 = call i32 @free(i64* %256)
%258 = load i64*, i64** %13
%259 = call i32 @free(i64* %258)
%260 = load i64*, i64** %14
%261 = call i32 @free(i64* %260)
%262 = load i64*, i64** %15
%263 = call i32 @free(i64* %262)
%264 = load i64*, i64** %16
%265 = call i32 @free(i64* %264)
%266 = load i64*, i64** %20
%267 = call i32 @free(i64* %266)
%268 = load i64*, i64** %21
%269 = call i32 @free(i64* %268)
store i32 -1, i32* %5
br label %458
270: ; preds = %247, %245, %243, %241, %239
store i32 0, i32* %11
br label %271
271: ; preds = %371, %270
%272 = load i32, i32* %11
%273 = load i32, i32* %45
%274 = icmp slt i32 %272, %273
br i1 %274, label %275, label %374
275: ; preds = %271
%276 = load i64, i64* %34
store i64 %276, i64* %36
%277 = load i64, i64* %35
store i64 %277, i64* %37
%278 = load i64*, i64** %17
%279 = load i32, i32* %11
%280 = sext i32 %279 to i64
%281 = getelementptr inbounds i64, i64* %278, i64 %280
%282 = load i64, i64* %281
store i64 %282, i64* %19
%283 = load i64, i64* %19
%284 = load i64*, i64** %20
%285 = load i32, i32* %11
%286 = sext i32 %285 to i64
%287 = getelementptr inbounds i64, i64* %284, i64 %286
%288 = load i64, i64* %287
%289 = or i64 %283, %288
store i64 %289, i64* %22
%290 = load i64, i64* %22
%291 = xor i64 %290, -1
store i64 %291, i64* %23
%292 = load i64, i64* %23
%293 = load i64*, i64** %21
%294 = load i32, i32* %11
%295 = sext i32 %294 to i64
%296 = getelementptr inbounds i64, i64* %293, i64 %295
%297 = load i64, i64* %296
%298 = or i64 %292, %297
store i64 %298, i64* %24
%299 = load i64, i64* %24
%300 = load i64*, i64** %20
%301 = load i32, i32* %11
%302 = sext i32 %301 to i64
%303 = getelementptr inbounds i64, i64* %300, i64 %302
%304 = load i64, i64* %303
%305 = xor i64 %299, %304
store i64 %305, i64* %25
%306 = load i64, i64* %24
%307 = load i64*, i64** %21
%308 = load i32, i32* %11
%309 = sext i32 %308 to i64
%310 = getelementptr inbounds i64, i64* %307, i64 %309
%311 = load i64, i64* %310
%312 = add i64 %306, %311
%313 = load i64, i64* %33
%314 = add i64 %312, %313
store i64 %314, i64* %30
%315 = load i64, i64* %30
%316 = load i64, i64* %24
%317 = icmp ult i64 %315, %316
br i1 %317, label %318, label %319
318: ; preds = %275
store i64 1, i64* %33
br label %319
319: ; preds = %318, %275
%320 = load i64, i64* %30
%321 = load i64, i64* %23
%322 = and i64 %320, %321
store i64 %322, i64* %31
%323 = load i64, i64* %31
%324 = load i64, i64* %25
%325 = xor i64 %323, %324
store i64 %325, i64* %26
%326 = load i64*, i64** %20
%327 = load i32, i32* %11
%328 = sext i32 %327 to i64
%329 = getelementptr inbounds i64, i64* %326, i64 %328
%330 = load i64, i64* %329
%331 = load i64, i64* %31
%332 = load i64*, i64** %21
%333 = load i32, i32* %11
%334 = sext i32 %333 to i64
%335 = getelementptr inbounds i64, i64* %332, i64 %334
%336 = load i64, i64* %335
%337 = and i64 %331, %336
%338 = or i64 %330, %337
store i64 %338, i64* %27
%339 = load i64, i64* %26
%340 = load i64, i64* %32
%341 = and i64 %339, %340
%342 = lshr i64 %341, 63
store i64 %342, i64* %35
%343 = load i64, i64* %27
%344 = load i64, i64* %32
%345 = and i64 %343, %344
%346 = lshr i64 %345, 63
store i64 %346, i64* %34
%347 = load i64, i64* %26
%348 = shl i64 %347, 1
%349 = load i64, i64* %37
%350 = add i64 %348, %349
store i64 %350, i64* %28
%351 = load i64, i64* %27
%352 = shl i64 %351, 1
%353 = load i64, i64* %36
%354 = add i64 %352, %353
store i64 %354, i64* %29
%355 = load i64, i64* %22
%356 = load i64, i64* %29
%357 = and i64 %355, %356
%358 = load i64*, i64** %20
%359 = load i32, i32* %11
%360 = sext i32 %359 to i64
%361 = getelementptr inbounds i64, i64* %358, i64 %360
store i64 %357, i64* %361
%362 = load i64, i64* %29
%363 = load i64, i64* %22
%364 = load i64, i64* %28
%365 = and i64 %363, %364
%366 = or i64 %362, %365
%367 = load i64*, i64** %21
%368 = load i32, i32* %11
%369 = sext i32 %368 to i64
%370 = getelementptr inbounds i64, i64* %367, i64 %369
store i64 %366, i64* %370
br label %371
371: ; preds = %319
%372 = load i32, i32* %11
%373 = add nsw i32 %372, 1
store i32 %373, i32* %11
br label %271
374: ; preds = %271
br label %375
375: ; preds = %374
%376 = load i32, i32* %10
%377 = add nsw i32 %376, 1
store i32 %377, i32* %10
br label %228
378: ; preds = %228
store i64 1, i64* %40
%379 = load i32, i32* %9
store i32 %379, i32* %42
%380 = load i32, i32* %9
store i32 %380, i32* %41
store i32 0, i32* %11
br label %381
381: ; preds = %439, %378
%382 = load i32, i32* %11
%383 = load i32, i32* %45
%384 = icmp slt i32 %382, %383
br i1 %384, label %385, label %442
385: ; preds = %381
%386 = load i64*, i64** %20
%387 = load i32, i32* %11
%388 = sext i32 %387 to i64
%389 = getelementptr inbounds i64, i64* %386, i64 %388
%390 = load i64, i64* %389
store i64 %390, i64* %38
%391 = load i64*, i64** %21
%392 = load i32, i32* %11
%393 = sext i32 %392 to i64
%394 = getelementptr inbounds i64, i64* %391, i64 %393
%395 = load i64, i64* %394
%396 = xor i64 %395, -1
store i64 %396, i64* %39
store i32 0, i32* %10
br label %397
397: ; preds = %435, %385
%398 = load i32, i32* %10
%399 = icmp slt i32 %398, 64
br i1 %399, label %400, label %438
400: ; preds = %397
%401 = load i32, i32* %10
%402 = load i32, i32* %11
%403 = or i32 %401, %402
%404 = icmp ne i32 %403, 0
br i1 %404, label %405, label %430
405: ; preds = %400
%406 = load i64, i64* %38
%407 = trunc i64 %406 to i32
%408 = sext i32 %407 to i64
%409 = load i64, i64* %40
%410 = and i64 %408, %409
%411 = load i32, i32* %41
%412 = sext i32 %411 to i64
%413 = sub i64 %412, %410
%414 = trunc i64 %413 to i32
store i32 %414, i32* %41
%415 = load i64, i64* %39
%416 = trunc i64 %415 to i32
%417 = sext i32 %416 to i64
%418 = load i64, i64* %40
%419 = and i64 %417, %418
%420 = load i32, i32* %41
%421 = sext i32 %420 to i64
%422 = add i64 %421, %419
%423 = trunc i64 %422 to i32
store i32 %423, i32* %41
%424 = load i32, i32* %41
%425 = load i32, i32* %42
%426 = icmp slt i32 %424, %425
br i1 %426, label %427, label %429
427: ; preds = %405
%428 = load i32, i32* %41
store i32 %428, i32* %42
br label %429
429: ; preds = %427, %405
br label %430
430: ; preds = %429, %400
%431 = load i64, i64* %38
%432 = lshr i64 %431, 1
store i64 %432, i64* %38
%433 = load i64, i64* %39
%434 = lshr i64 %433, 1
store i64 %434, i64* %39
br label %435
435: ; preds = %430
%436 = load i32, i32* %10
%437 = add nsw i32 %436, 1
store i32 %437, i32* %10
br label %397
438: ; preds = %397
br label %439
439: ; preds = %438
%440 = load i32, i32* %11
%441 = add nsw i32 %440, 1
store i32 %441, i32* %11
br label %381
442: ; preds = %381
%443 = load i64*, i64** %12
%444 = call i32 @free(i64* %443)
%445 = load i64*, i64** %13
%446 = call i32 @free(i64* %445)
%447 = load i64*, i64** %14
%448 = call i32 @free(i64* %447)
%449 = load i64*, i64** %15
%450 = call i32 @free(i64* %449)
%451 = load i64*, i64** %16
%452 = call i32 @free(i64* %451)
%453 = load i64*, i64** %20
%454 = call i32 @free(i64* %453)
%455 = load i64*, i64** %21
%456 = call i32 @free(i64* %455)
%457 = load i32, i32* %42
store i32 %457, i32* %5
br label %458
458: ; preds = %442, %249, %187, %48
%459 = load i32, i32* %5
ret i32 %459
}

LLVM IR (-O2):
@.str = [61 x i8] c"\0AError, non-ACGTN character read at position %d in string:%c\00"
@.str.1 = [46 x i8] c"\0AError, non-ACGTN character read in string:%c\00"
define i32 @Edit_Distance_multiple_word_NoEndPenaltySeq1(i8* nocapture %0, i8* nocapture %1, i32 %2, i32 %3) {
%5 = icmp eq i32 %3, 0
br i1 %5, label %208, label %6
6: ; preds = %4
%7 = icmp sgt i32 %2, 63
br i1 %7, label %8, label %16
8: ; preds = %6
%9 = add nsw i32 %2, -63
%10 = lshr i32 %9, 6
%11 = mul nsw i32 %10, -64
%12 = add nsw i32 %11, %9
%13 = icmp slt i32 %12, 1
%14 = select i1 %13, i32 1, i32 2
%15 = add nuw nsw i32 %14, %10
br label %16
16: ; preds = %6, %8
%17 = phi i32 [ %15, %8 ], [ 1, %6 ]
%18 = tail call i64 @calloc(i32 %17, i32 8)
%19 = inttoptr i64 %18 to i64*
%20 = tail call i64 @calloc(i32 %17, i32 8)
%21 = inttoptr i64 %20 to i64*
%22 = tail call i64 @calloc(i32 %17, i32 8)
%23 = inttoptr i64 %22 to i64*
%24 = tail call i64 @calloc(i32 %17, i32 8)
%25 = inttoptr i64 %24 to i64*
%26 = tail call i64 @calloc(i32 %17, i32 8)
%27 = inttoptr i64 %26 to i64*
%28 = tail call i64 @calloc(i32 %17, i32 8)
%29 = inttoptr i64 %28 to i64*
%30 = tail call i64 @calloc(i32 %17, i32 8)
%31 = inttoptr i64 %30 to i64*
%32 = sext i32 %2 to i64
%33 = zext i32 %17 to i64
br label %37
34: ; preds = %86
%35 = add i32 %39, 64
%36 = icmp eq i64 %46, %33
br i1 %36, label %91, label %37
37: ; preds = %16, %34
%38 = phi i64 [ 0, %16 ], [ %46, %34 ]
%39 = phi i32 [ 0, %16 ], [ %35, %34 ]
%40 = sext i32 %39 to i64
%41 = getelementptr inbounds i64, i64* %19, i64 %38
store i64 0, i64* %41
%42 = getelementptr inbounds i64, i64* %21, i64 %38
store i64 0, i64* %42
%43 = getelementptr inbounds i64, i64* %23, i64 %38
store i64 0, i64* %43
%44 = getelementptr inbounds i64, i64* %25, i64 %38
store i64 0, i64* %44
%45 = getelementptr inbounds i64, i64* %27, i64 %38
store i64 0, i64* %45
%46 = add nuw nsw i64 %38, 1
%47 = trunc i64 %46 to i32
%48 = shl nsw i32 %47, 6
%49 = icmp ne i64 %38, 0
br label %50
50: ; preds = %37, %86
%51 = phi i64 [ %40, %37 ], [ %88, %86 ]
%52 = phi i64 [ 1, %37 ], [ %87, %86 ]
%53 = icmp sgt i64 %51, %32
br i1 %53, label %86, label %54
54: ; preds = %50
%55 = icmp ne i64 %51, 0
%56 = select i1 %55, i1 true, i1 %49
br i1 %56, label %57, label %84
57: ; preds = %54
%58 = add nsw i64 %51, -1
%59 = getelementptr inbounds i8, i8* %0, i64 %58
%60 = load i8, i8* %59
%61 = sext i8 %60 to i32
switch i32 %61, label %66 [
i32 65, label %80
i32 67, label %62
i32 71, label %63
i32 84, label %64
i32 78, label %65
]
62: ; preds = %57
br label %80
63: ; preds = %57
br label %80
64: ; preds = %57
br label %80
65: ; preds = %57
br label %80
66: ; preds = %57
%67 = trunc i64 %51 to i8
%68 = and i64 %51, 4294967295
%69 = getelementptr inbounds i8, i8* %0, i64 %68
%70 = load i8, i8* %69
%71 = sext i8 %70 to i32
%72 = tail call i32 (i8*, i8, ...) @printf(i8* getelementptr inbounds ([61 x i8], [61 x i8]* @.str, i64 0, i64 0), i8 signext %67, i32 %71)
%73 = tail call i32 @free(i64* %19)
%74 = tail call i32 @free(i64* %21)
%75 = tail call i32 @free(i64* %23)
%76 = tail call i32 @free(i64* %25)
%77 = tail call i32 @free(i64* %27)
%78 = tail call i32 @free(i64* %29)
%79 = tail call i32 @free(i64* %31)
br label %208
80: ; preds = %57, %65, %64, %63, %62
%81 = phi i64* [ %42, %62 ], [ %43, %63 ], [ %44, %64 ], [ %45, %65 ], [ %41, %57 ]
%82 = load i64, i64* %81
%83 = or i64 %82, %52
store i64 %83, i64* %81
br label %84
84: ; preds = %80, %54
%85 = shl i64 %52, 1
br label %86
86: ; preds = %50, %84
%87 = phi i64 [ %85, %84 ], [ %52, %50 ]
%88 = add nsw i64 %51, 1
%89 = trunc i64 %88 to i32
%90 = icmp ugt i32 %48, %89
br i1 %90, label %50, label %34
91: ; preds = %34
store i64 1, i64* %29
store i64 1, i64* %31
%92 = icmp sgt i32 %3, 0
br i1 %92, label %93, label %152
93: ; preds = %91
%94 = zext i32 %3 to i64
br label %95
95: ; preds = %93, %149
%96 = phi i64 [ 0, %93 ], [ %150, %149 ]
%97 = getelementptr inbounds i8, i8* %1, i64 %96
%98 = load i8, i8* %97
%99 = sext i8 %98 to i32
switch i32 %99, label %104 [
i32 65, label %113
i32 67, label %100
i32 71, label %101
i32 84, label %102
i32 78, label %103
]
100: ; preds = %95
br label %113
101: ; preds = %95
br label %113
102: ; preds = %95
br label %113
103: ; preds = %95
br label %113
104: ; preds = %95
%105 = tail call i32 (i8*, i8, ...) @printf(i8* getelementptr inbounds ([46 x i8], [46 x i8]* @.str.1, i64 0, i64 0), i8 signext %98)
%106 = tail call i32 @free(i64* %19)
%107 = tail call i32 @free(i64* %21)
%108 = tail call i32 @free(i64* %23)
%109 = tail call i32 @free(i64* %25)
%110 = tail call i32 @free(i64* %27)
%111 = tail call i32 @free(i64* %29)
%112 = tail call i32 @free(i64* %31)
br label %208
113: ; preds = %95, %103, %102, %101, %100
%114 = phi i64* [ %27, %103 ], [ %25, %102 ], [ %23, %101 ], [ %21, %100 ], [ %19, %95 ]
br label %115
115: ; preds = %113, %115
%116 = phi i64 [ 0, %113 ], [ %147, %115 ]
%117 = phi i64 [ 0, %113 ], [ %138, %115 ]
%118 = phi i64 [ 1, %113 ], [ %139, %115 ]
%119 = phi i64 [ 0, %113 ], [ %133, %115 ]
%120 = getelementptr inbounds i64, i64* %114, i64 %116
%121 = load i64, i64* %120
%122 = getelementptr inbounds i64, i64* %29, i64 %116
%123 = load i64, i64* %122
%124 = or i64 %123, %121
%125 = xor i64 %124, -1
%126 = getelementptr inbounds i64, i64* %31, i64 %116
%127 = load i64, i64* %126
%128 = or i64 %127, %125
%129 = xor i64 %128, %123
%130 = add i64 %127, %119
%131 = add i64 %130, %128
%132 = icmp ult i64 %131, %128
%133 = select i1 %132, i64 1, i64 %119
%134 = and i64 %131, %125
%135 = xor i64 %129, %134
%136 = and i64 %134, %127
%137 = or i64 %136, %123
%138 = lshr i64 %135, 63
%139 = lshr i64 %137, 63
%140 = shl i64 %135, 1
%141 = or i64 %140, %117
%142 = shl i64 %137, 1
%143 = or i64 %142, %118
%144 = and i64 %143, %124
store i64 %144, i64* %122
%145 = and i64 %141, %124
%146 = or i64 %143, %145
store i64 %146, i64* %126
%147 = add nuw nsw i64 %116, 1
%148 = icmp eq i64 %147, %33
br i1 %148, label %149, label %115
149: ; preds = %115
%150 = add nuw nsw i64 %96, 1
%151 = icmp eq i64 %150, %94
br i1 %151, label %152, label %95
152: ; preds = %149, %91
br label %153
153: ; preds = %152, %197
%154 = phi i64 [ %198, %197 ], [ 0, %152 ]
%155 = phi i32 [ %192, %197 ], [ %3, %152 ]
%156 = phi i32 [ %190, %197 ], [ %3, %152 ]
%157 = getelementptr inbounds i64, i64* %29, i64 %154
%158 = load i64, i64* %157
%159 = getelementptr inbounds i64, i64* %31, i64 %154
%160 = load i64, i64* %159
%161 = xor i64 %160, -1
%162 = trunc i64 %154 to i32
br label %163
163: ; preds = %180, %153
%164 = phi i32 [ 0, %153 ], [ %195, %180 ]
%165 = phi i32 [ %155, %153 ], [ %192, %180 ]
%166 = phi i32 [ %156, %153 ], [ %190, %180 ]
%167 = phi i64 [ %161, %153 ], [ %194, %180 ]
%168 = phi i64 [ %158, %153 ], [ %193, %180 ]
%169 = or i32 %164, %162
%170 = icmp eq i32 %169, 0
br i1 %170, label %180, label %171
171: ; preds = %163
%172 = trunc i64 %168 to i32
%173 = and i32 %172, 1
%174 = sub i32 %166, %173
%175 = trunc i64 %167 to i32
%176 = and i32 %175, 1
%177 = add i32 %176, %174
%178 = icmp slt i32 %177, %165
%179 = select i1 %178, i32 %177, i32 %165
br label %180
180: ; preds = %163, %171
%181 = phi i32 [ %166, %163 ], [ %177, %171 ]
%182 = phi i32 [ %165, %163 ], [ %179, %171 ]
%183 = trunc i64 %168 to i32
%184 = lshr i32 %183, 1
%185 = and i32 %184, 1
%186 = sub i32 %181, %185
%187 = trunc i64 %167 to i32
%188 = lshr i32 %187, 1
%189 = and i32 %188, 1
%190 = add i32 %189, %186
%191 = icmp slt i32 %190, %182
%192 = select i1 %191, i32 %190, i32 %182
%193 = lshr i64 %168, 2
%194 = lshr i64 %167, 2
%195 = add nuw nsw i32 %164, 2
%196 = icmp eq i32 %195, 64
br i1 %196, label %197, label %163
197: ; preds = %180
%198 = add nuw nsw i64 %154, 1
%199 = icmp eq i64 %198, %33
br i1 %199, label %200, label %153
200: ; preds = %197
%201 = tail call i32 @free(i64* %19)
%202 = tail call i32 @free(i64* %21)
%203 = tail call i32 @free(i64* %23)
%204 = tail call i32 @free(i64* %25)
%205 = tail call i32 @free(i64* %27)
%206 = tail call i32 @free(i64* %29)
%207 = tail call i32 @free(i64* %31)
br label %208
208: ; preds = %4, %200, %104, %66
%209 = phi i32 [ -1, %66 ], [ -1, %104 ], [ %192, %200 ], [ 0, %4 ]
ret i32 %209
}