我已经找到了解决方案。

我做了一些基准测试与是一个ASCII文件3.050 KB和38803 lines。与搜索byte array的22 bytes在文件的最后一行，我得到了在有关结果2.28秒（在慢/旧机）。

public static long FindPosition(Stream stream, byte[] byteSequence)
{
    if (byteSequence.Length > stream.Length)
        return -1;

    byte[] buffer = new byte[byteSequence.Length];

    using (BufferedStream bufStream = new BufferedStream(stream, byteSequence.Length))
    {
        int i;
        while ((i = bufStream.Read(buffer, 0, byteSequence.Length)) == byteSequence.Length)
        {
            if (byteSequence.SequenceEqual(buffer))
                return bufStream.Position - byteSequence.Length;
            else
                bufStream.Position -= byteSequence.Length - PadLeftSequence(buffer, byteSequence);
        }
    }

    return -1;
}

private static int PadLeftSequence(byte[] bytes, byte[] seqBytes)
{
    int i = 1;
    while (i < bytes.Length)
    {
        int n = bytes.Length - i;
        byte[] aux1 = new byte[n];
        byte[] aux2 = new byte[n];
        Array.Copy(bytes, i, aux1, 0, n);
        Array.Copy(seqBytes, aux2, n);
        if (aux1.SequenceEqual(aux2))
            return i;
        i++;
    }
    return i;
}