k, fine. to be very clear, i didnt want to confuse you all with my whole program,the ones which you said as UNUSED VALUES are not unused values, but i will be using it while printing the results later.so all i want to process now is the SEQUENCE. that is the string(a continous stretch of alphabets)which is next to the accessions line. so when i grep it and store it in a seperate array, and when i print the array (inside the loop) i am getting the output something like this

MGDVEKGKKIFIMKCSQCHTVEMGDVEKGGKHKTGPNLHGLFGRKTGQAPGYSYTAANKNKGIIWGEDTL
+MEYLENPKKYIP
MGDVEKGKKIFIMKCSQCHTVEMGDVEKGGKHKTGPNLHGLFGRKTGQAPGYSYTAANKNKGIIWGEDTL
+MEYLENPKKYIP
MGDVEKGKKIFIMKCSQCHTVEMGDVEKGGKHKTGPNLHGLFGRKTGQAPGYSYTAANKNKGIIWGEDTL
+MEYLENPKKYIP
MGDVEKGKKIFIMKCSQCHTVEMGDVEKGGKHKTGPNLHGLFGRKTGQAPGYSYTAANKNKGIIWGEDTL
+MEYLENPKKYIP
MGDVEKGKKIFIMKCSQCHTVEMGDVEKGGKHKTGPNLHGLFGRKTGQAPGYSYTAANKNKGIIWGEDTL
+MEYLENPKKYIP
GDVEKGKKIFIMKCSQCHTVEKGSSSKHKSSSTGPNLHGLFGRKTGQAPGYSYTAANKNKGIIWGED
GDVEKGKKIFIMKCSQCHTVEKGSSSKHKSSSTGPNLHGLFGRKTGQAPGYSYTAANKNKGIIWGED
GDVEKGKKIFIMKCSQCHTVEKGSSSKHKSSSTGPNLHGLFGRKTGQAPGYSYTAANKNKGIIWGED
GDVEKGKKIFIMKCSQCHTVEKGSSSKHKSSSTGPNLHGLFGRKTGQAPGYSYTAANKNKGIIWGED
GDVEKGKKIFIMKCSQCHTVEKGSSSKHKSSSTGPNLHGLFGRKTGQAPGYSYTAANKNKGIIWGED
GDVEKGKKIFIMKCSQCHTVEKGGSSSSKHKTGPNLHGLFGAAAAAAAARKTGQAPGYSYTAANKSSSSN
+KGITWGEDTLMEYLENPKKYIPGTKMIFVGIKKKEE
GDVEKGKKIFIMKCSQCHTVEKGGSSSSKHKTGPNLHGLFGAAAAAAAARKTGQAPGYSYTAANKSSSSN
+KGITWGEDTLMEYLENPKKYIPGTKMIFVGIKKKEE
GDVEKGKKIFIMKCSQCHTVEKGGSSSSKHKTGPNLHGLFGAAAAAAAARKTGQAPGYSYTAANKSSSSN
+KGITWGEDTLMEYLENPKKYIPGTKMIFVGIKKKEE
GDVEKGKKIFIMKCSQCHTVEKGGSSSSKHKTGPNLHGLFGAAAAAAAARKTGQAPGYSYTAANKSSSSN
+KGITWGEDTLMEYLENPKKYIPGTKMIFVGIKKKEE
GDVEKGKKIFIMKCSQCHTVEKGGSSSSKHKTGPNLHGLFGAAAAAAAARKTGQAPGYSYTAANKSSSSN
+KGITWGEDTLMEYLENPKKYIPGTKMIFVGIKKKEE
GDVFKGKRIFIMKCSQCHTVESSSSKGGKHKTGPNLHGLFGSSSSSSSSSSR
[download]

when i print the array outside the loop, either its printing the last string alone, or, removes the repeating alphabets from the string and printin a result like this.

MGDVEKIFCSQHTPNLRAYW
MGDVEKIFCSQHTPNLRAYW
MGDVEKIFCSQHTPNLRAYW
MGDVEKIFCSQHTPNLRAYW
MGDVEKIFCSQHTPNLRAYW
GDVEKIFMCSQHTPNLRAYW
GDVEKIFMCSQHTPNLRAYW
GDVEKIFMCSQHTPNLRAYW
GDVEKIFMCSQHTPNLRAYW
GDVEKIFMCSQHTPNLRAYW
GDVEKIFMCSQHTPNLARYW
GDVEKIFMCSQHTPNLARYW
GDVEKIFMCSQHTPNLARYW
GDVEKIFMCSQHTPNLARYW
GDVEKIFMCSQHTPNLARYW
GDVFKRIMCSQHTEPNL
[download]

but the result which i need is:

MGDVEKGKKIFIMKCSQCHTVEMGDVEKGGKHKTGPNLHGLFGRKTGQAPGYSYTAANKNKGIIWGEDTL
+MEYLENPKKYIP
GDVEKGKKIFIMKCSQCHTVEKGSSSKHKSSSTGPNLHGLFGRKTGQAPGYSYTAANKNKGIIWGED
GDVEKGKKIFIMKCSQCHTVEKGGSSSSKHKTGPNLHGLFGAAAAAAAARKTGQAPGYSYTAANKSSSSN
+KGITWGEDTLMEYLENPKKYIPGTKMIFVGIKKKEE
GDVFKGKRIFIMKCSQCHTVESSSSKGGKHKTGPNLHGLFGSSSSSSSSSSR
[download]

and i need all this as 4 elements in the same array. i hope u got it.