#pragma warning(disable:4786)
#include <algorithm>
#include <iostream>
#include <fstream>
#include <cstring>
#include <cstdlib>
#include <cstdio>
#include <cmath>
#include <queue>
#include <stack>
#include <set>
#include <map>
#include <cinio.h>
#include <string>
using namespace std;
const long  maxn = 1048580;
const int INF = 0x3fffff;
const double EPS = 1e-6;
const double PI = 3.1415926;
typedef  long  ll;
int dx[4] = {0,0,1,-1};
int dy[4] = {1,-1,0,0};

int k;
typedef struct node    //′￠Öμ
{
    int add;
    struct node *next;
} node,*Rlink;
Rlink head[maxn];
void List_insert(int add,int data)                  //á′±íÖD2åèëμØÖ·
{
    if(head[add]==NULL)
    {
        head[add] = (node *)malloc(sizeof(node));
        head[add]->add = data;
        head[add]->next = NULL;
    }
    else
    {
        node *p = head[add];
        while(p->next)
            p=p->next;
        node *q = (node *)malloc(sizeof(node));
        q->add = data;
        q->next = NULL;
        p->next = q;
    }
}

char str[1048580][101];
char lstr[110000000];
int hash(char *strr);

struct Trie
{
    int next[1048580][101],fail[1048580],end[1048580];
    int root,L;
    int newnode()
    {
        for(int i = 0; i < 101; i++)
            next[L][i] = -1;
        end[L++] = -1;
        return L-1;
    }
    void init()
    {
        L = 0;
        root = newnode();
    }
    void insert(char s[],int id)
    {
        int len = strlen(s);
        int now = root;
        for(int i = 0; i < len; i++)
        {
            if(next[now][s[i]] == -1)
                next[now][s[i]] = newnode();
            now = next[now][s[i]];
        }
        end[now] = id;
    }
    void build()
    {
        queue<int>Q;
        fail[root] = root;
        for(int i = 0; i < 101; i++)
            if(next[root][i] == -1)
                next[root][i] = root;
            else
            {
                fail[next[root][i]] = root;
                Q.push(next[root][i]);
            }
        while(!Q.empty())
        {
            int now = Q.front();
            Q.pop();
            for(int i = 0; i < 101; i++)
                if(next[now][i] == -1)
                    next[now][i]=next[fail[now]][i];
                else
                {
                    fail[next[now][i]]=next[fail[now]][i];
                    Q.push(next[now][i]);
                }
        }
    }
    int num[1048580];//¼Ç¼¸öêy
    vector<int>post[1048580];//¼Ç¼λÖÃ

    void query(char buf[],int n)
    {
        for(int i = 0; i < n; i++)
            num[i] = 0,post[i].clear();
        int len=strlen(buf);
        int now=root;
        for( i=0; i<len; i++)
        {
            now=next[now][buf[i]];
            int temp = now;
            while( temp != root )
            {
                if(end[temp] != -1)
                {
                    num[end[temp]]++;
                    post[end[temp]].push_back(i);
                }
                temp = fail[temp];
            }
        }
        for(i = 0; i < n; i++)
        {
            if(num[i] > 0)
            {
                int add = hash(str[i]);    //′æ′￠Ôúêy×éÖD
                for(int j=0; j<post[i].size(); j++)
                {
                    List_insert(add,post[i][j]+1-k);      //
                }
            }
        }
    }
};
Trie ac;

int hash(char *strr)
{
    int len = strlen(strr);
    int add = 0;  //μØÖ·
    int base = 1; //½øÖÆ
    for(int i=len-1; i>=0; i--)
    {
        switch(strr[i])
        {
        case 'A':
            add += 0*base;
            break;
        case 'T':
            add += 1*base;
            break;
        case 'G':
            add += 2*base;
            break;
        case 'C':
            add += 3*base;
            break;
        }
        base*=4;
    }
    return add;
}

void substr(char *st,char *ss,int i,int j)  //i¿aê¼½Øè¡j¸ö×Ö·û,èó½østÖD
{
    for(int k=0; k<j; k++)
        st[k] = ss[k+i];
    st[j] = '\0';
}

void Index(char *s)
{
    int add = hash(s);
    node *p = head[add];
    while(p)
    {
        printf("Ä￡ê½′®ËùÔúDNADòáDoÅÎa: %d,ËùÔúμÄϱêÎa: %d\n",p->add/101+1,p->add%101+1);
        p=p->next;
    }
}

int main()
{
    printf("Çëêäèëò»¸öKÖμ:\n");
    scanf("%d",&k);
    map <string,int> map;       //è￥ÖØ
    string ss;
    char tmp[102];
    ac.init();
    int i=0;
    int cnt=0;   //¼Ç¼Ä￡ê½′®¸öêy
    ifstream in("C:\\Users\\Administrator\\Desktop\\KMP\\solexa_100_170_1.fa");  //Îļt¶áè¡
    if(in)
    {
        while(getline(in,ss))
        {
            ss.copy(tmp,100,0);
            tmp[100] = '*';          //½«2»í¬DDμÄ×Ö·û′®·Ö¸ô¿a,±üÃa¿çDDÆ￥Åä3é1|
            tmp[101] = '\0';
            strcat(lstr,tmp);
            for(int j=0; j<=100-k; j++)
            {
                string moshi = ss.substr(j,k);
                if(map[moshi]==1) continue;       //òѾ-2åèë1yμÄÄ￡ê½′®2»»áÔù2åèë
                substr(str[cnt],tmp,j,k);
                ac.insert(str[cnt],cnt);
                cnt++;
                map[moshi] = 1;                   //2åèë±ê¼Ç
            }
            i++;
        }
    }
    ac.build();   //ac×Ô¶ˉ»ú½¨á￠
    ac.query(lstr,cnt);
    char l[101];
    printf("ÇëêäèëÄúòa2éÑˉμÄk-mer:\n");
    while(~scanf("%s",l))
        Index(l);
    return 0;
}

好多火星文

好大的数组，我肯定看不懂

char str[1048580][101];

 char lstr[110000000];

 int hash(char *strr);


 struct Trie

 {
     int next[1048580][101],fail[1048580],end[1048580];

太恐怖了  怎么这么长

从软件上粘贴过来时，汉字就成了火星文了

打个包发会好点吧，代码太多的话