Trying to run Timer1 in ATmega2560 with assembly I have a slight problem with Timer1 in arduino (ATmega2560) while coding it in assembly. I try to run the Timer1 in CTC mode - I configure everything well in my opinion, but the TCNT1 just doesn't increment each clock cycle, as it should. I checked the registers in Atmel Studio and everything seems okay, but maybe I forgot about something?

Here is the code 

.ORG 0
jmp start

.ORG 0x22
call isr_toggle_PA0

.ORG 0x400
start:
LDI R16, HIGH(RAMEND)
OUT SPH, R16
LDI R16, LOW(RAMEND)
OUT SPL, R16 ; initialize stack pointer
clr r16

ldi r16, 0xff
out DDRA, r16 ; port A output
ldi r16, 0x00
out DDRD, r16 ; port D input
clr r16

ldi r20, 1&lt;&lt;OCIE1A
sts TIMSK1, r20 ; enable Timer1 A comapre match interrupt
sei

ldi r20, HIGH(25000)
sts OCR1AH, r20
ldi r20, LOW(25000)
sts OCR1AL, r20

ldi r20, 0b00000010 ; CTC mode, int clk;
sts TCCR1A, r20     
ldi r20, 0b000000101 ; prescaler /1024
sts TCCR1B, r20
ldi r20, 0
sts TCCR1C, r20

; --- start main
main:


inc r16
rjmp main
; --- end main

isr_toggle_PA0: // toggle bit on PA0
    ldi r16,0x00000001
    in r17, PORTA
    eor r17,r16
    out PORTA, r17
    reti


Thank you and have a good day :)
Here:

ldi r20, 0b00000010 ; CTC mode, int clk;
sts TCCR1A, r20     
ldi r20, 0b000000101 ; prescaler /1024
sts TCCR1B, r20


you are setting the bit WGM11 on TCCR1A. The timer then runs in mode 2 (PWM, Phase Correct, 9-bit) rather than mode 4 (CTC).