     }
 
     __syncthreads();
-    sequence += sequence_lengths[0]; // increment the pointer so it is pointing to correct sequence data
 
     back_time += (clock64() - t0);
 

    {
        //printf("running window %d seq %d / %d\n", block_idx, s, num_sequences_in_window);
        uint16_t seq_len = sequence_lengths[s];
/*
        if (thread_idx == 0)
            printf("seq len is %i for sequence %i\n", seq_len, s);

                printf("Sequence len %d is greater than max matrix size %d\n", seq_len, CUDAPOA_MAX_NODES_PER_WINDOW);
                return;
            }


        }
        long long int start = clock64();
