hi graff, thanks for the reply. but,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 MGDVEKGKKIFIMKCSQCHTVEMGDVEKGGKHKTGPNLHGLFGRKTGQAPGYSY
+TAANKNKGIIWGEDTL +MEYLENPKKYIP MGDVEKGKKIFIMKCSQCHTVEMGDVEKGGKHKTGPNL
+HGLFGRKTGQAPGYSYTAANKNKGIIWGEDTL +MEYLENPKKYIP MGDVEKGKKIFIMKCSQCHTVE
+MGDVEKGGKHKTGPNLHGLFGRKTGQAPGYSYTAANKNKGIIWGEDTL +MEYLENPKKYIP MGDVEK
+GKKIFIMKCSQCHTVEMGDVEKGGKHKTGPNLHGLFGRKTGQAPGYSYTAANKNKGIIWGEDTL +MEY
+LENPKKYIP GDVEKGKKIFIMKCSQCHTVEKGSSSKHKSSSTGPNLHGLFGRKTGQAPGYSYTAANKN
+KGIIWGED GDVEKGKKIFIMKCSQCHTVEKGSSSKHKSSSTGPNLHGLFGRKTGQAPGYSYTAANKNK
+GIIWGED GDVEKGKKIFIMKCSQCHTVEKGSSSKHKSSSTGPNLHGLFGRKTGQAPGYSYTAANKNKG
+IIWGED GDVEKGKKIFIMKCSQCHTVEKGSSSKHKSSSTGPNLHGLFGRKTGQAPGYSYTAANKNKGI
+IWGED GDVEKGKKIFIMKCSQCHTVEKGSSSKHKSSSTGPNLHGLFGRKTGQAPGYSYTAANKNKGII
+WGED GDVEKGKKIFIMKCSQCHTVEKGGSSSSKHKTGPNLHGLFGAAAAAAAARKTGQAPGYSYTAAN
+KSSSSN +KGITWGEDTLMEYLENPKKYIPGTKMIFVGIKKKEE GDVEKGKKIFIMKCSQCHTVEKGG
+SSSSKHKTGPNLHGLFGAAAAAAAARKTGQAPGYSYTAANKSSSSN +KGITWGEDTLMEYLENPKKYI
+PGTKMIFVGIKKKEE GDVEKGKKIFIMKCSQCHTVEKGGSSSSKHKTGPNLHGLFGAAAAAAAARKTG
+QAPGYSYTAANKSSSSN +KGITWGEDTLMEYLENPKKYIPGTKMIFVGIKKKEE GDVEKGKKIFIMK
+CSQCHTVEKGGSSSSKHKTGPNLHGLFGAAAAAAAARKTGQAPGYSYTAANKSSSSN +KGITWGEDTL
+MEYLENPKKYIPGTKMIFVGIKKKEE GDVEKGKKIFIMKCSQCHTVEKGGSSSSKHKTGPNLHGLFGA
+AAAAAAARKTGQAPGYSYTAANKSSSSN +KGITWGEDTLMEYLENPKKYIPGTKMIFVGIKKKEE GD
+VFKGKRIFIMKCSQCHTVESSSSKGGKHKTGPNLHGLFGSSSSSSSSSSR
[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 MGDVEKI
+FCSQHTPNLRAYW MGDVEKIFCSQHTPNLRAYW GDVEKIFMCSQHTPNLRAYW GDVEKIFMCSQHT
+PNLRAYW GDVEKIFMCSQHTPNLRAYW GDVEKIFMCSQHTPNLRAYW GDVEKIFMCSQHTPNLRAY
+W GDVEKIFMCSQHTPNLARYW GDVEKIFMCSQHTPNLARYW GDVEKIFMCSQHTPNLARYW GDVE
+KIFMCSQHTPNLARYW GDVEKIFMCSQHTPNLARYW GDVFKRIMCSQHTEPNL
[download]

but the result which i need is:

MGDVEKGKKIFIMKCSQCHTVEMGDVEKGGKHKTGPNLHGLFGRKTGQAPGYSYTAANKNKGIIWGEDTL
+ +MEYLENPKKYIP GDVEKGKKIFIMKCSQCHTVEKGSSSKHKSSSTGPNLHGLFGRKTGQAPGYSYT
+AANKNKGIIWGED GDVEKGKKIFIMKCSQCHTVEKGGSSSSKHKTGPNLHGLFGAAAAAAAARKTGQA
+PGYSYTAANKSSSSN +KGITWGEDTLMEYLENPKKYIPGTKMIFVGIKKKEE GDVFKGKRIFIMKCS
+QCHTVESSSSKGGKHKTGPNLHGLFGSSSSSSSSSSR
[download]

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

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