Seq1=ACGTGCCC
Seq2=CCCCCGTGTGTGT
Seq_merged=ACGTGCCCCCGTGTGTGT

#include <stdio.h>
#include <stdlib.h>
#include <string.h>

#define MAXLEN 4096

//strmerg was from: http://effprog.wordpress.com/2010/11/18/concatenation-of-two-strings-omitting-overlapping-string/
char *strmerg(char *dst, const char *src)
{
    size_t dstLen = strlen(dst);
    size_t srcLen = strlen(src);

    char *p = dst + dstLen + srcLen;            /* Pointer to the end of the concatenated string */
    const char *q = src + srcLen - 1;            /* Pointer to the last character of the src */
    char *r = dst + dstLen - 1;                    /* Temp Pointer to the last character of the dst */
    char *end = r;                                /* Permanent Pointer to the last character of the dst */
    *p = '\0';                                    /*terminating the concatened string with NULL character */

    while (q >= src) 
{        /*Copy src in reverse */
    if (*r == *q) {                                /*Till it matches with the src, decrement r */
        r--;
    } else {
        r = end;
        if (*r == *q) {
        r--;
        }
    }

    *p-- = *q--;
    }

    while (r >= dst)                            /*Copy dst, ending with r */
    *p-- = *r--;

    return p + 1;
}

int main(int argc, char **argv)
{
    char *str1, *str2;        //Original two strings
    char *str3;                //resulting string

    str1 = malloc(sizeof(char) * MAXLEN);    //allocate memory
    str2 = malloc(sizeof(char) * MAXLEN);    //allocate memory

    str3 = malloc(sizeof(char) * MAXLEN * 2);    //allocate memory, maximum space needed is the sum of the two original string lengths

    if (argc != 3) {
    printf("Error! \nUsage: ./arg[0]=program argv[1]=string1 argv[2]=string2\n");
    exit(EXIT_FAILURE);
    }

    strcpy(str1, argv[1]);
    strcpy(str2, argv[2]);

    printf("Input strings are: \nSeq1=%s\nSeq2=%s\n", str1, str2);

    str3=strmerg(str1, str2);
    printf("\nConcatenated string is: Seq_merged=%s\n", str3);
/*Some problem with these free(), do not know why?
free(str1);
free(str2);
free(str3);
*/
    return 0;
}

./prog ACGTGCCC CCCCCGTGTGTGT 
Seq1=ACGTGCCC
Seq2=CCCCCGTGTGTGT 
Seq_merged=ACGTGCCCCCCGTGTGTGT 
./prog ACGTGatcg atcgCCGTGTGTGT
Seq1= ACGTGatcg
Seq2= atcgCCGTGTGTGT
Seq_merged=ACGTGatcgCCGTGTGTGT
./prog ACGTGatatat atatCCGTGTGTGT
Seq1=ACGTGatatat
Seq2=atatCCGTGTGTGT
Seq_merged=ACGTGatatatatatCCGTGTGTGT