Untested awk..

awk '{a[$1 FS $2]++}END{for(x in a)print x,a[x]}' infile > outfile

Ha ha ...every time I see a thread like this I just wait for Ygor to respond..He's definitely one with Awk!

YGOR your close to the result that i wanted

this is the output of your awk
YRLNCA11-SL1 DMT8a4 13

it should have been
YRLNCA11-SL1 DMT8a4 5 2
YRLNCA11-SL1 DMT8a4 6 11

the first 2 fields are still the same but the 2nd to the last is different - 5 and 6

5 appeared 2x
and 6 appeared 11x

almost there ... but I could still use that awk though..

THANKS

You could probably change Ygor's awk to

awk '{a[$1 FS $2 FS $3]++}END{for(x in a)print x,a[x]}' infile > outfile

to use the first three fields as the index

Cheers
ZB

Please can somebody explain the awk solution of ygor and zazzybob, i tried to play with it on my machine to make some sence of it but it is not clear yet...
i am an awk lover but still biginner.

The awk program uses an associative array "a" to hold the count for each key. The key is the first 2 or 3 fields. At the end of the input file, loop thru the array and print each key with its count.

It's not mandatory to use awk, you could use shell utils, e.g....

$ sort infile | cut -d' ' -f-3 | uniq -c | while read A B C D; do echo $B $C $D $A; done
ALBQNMMA-SL1 DMT8a4 12 1
ALBQNMMA-SL1 DMT8a4 3 4
FUTNCA01-SL1 DMT8a4 5 6
FUTNCA01-SL1 DMT8a4 6 3

THANK YOU TO EVERYBODY THAT HELPED -- LEARNED A LOT!!!