Reading input alignment file to find conserved blocks of secondary structure

The input structure based alignment from Comparer
_____________________________________________

>P1;d1jeqa1
CCHHHHHHHHHCCCHHHCCHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHCC----------------------

>P1;d1kcfa1
----------------CCCHHHHHHHHHHCCCCCCC---CCCCCCCCCCCCC---------------------

>P1;d1v66a-
----CCCCCHHHHHHCCCCHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHCC----

>P1;d1zrja1
------------CCHHHCCHHHHHHHHHHHCCCCCCCHHHHHHHHHHHC------------------------

>P1;d4uzwa1
------------CHHHHCCHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHH------------HCCCCCCCC
PSA

>P1;d1jeqa1
288a5086327795058075630550065191a33a847301620474187----------------------

>P1;d1kcfa1
----------------b6747703530665a26599---5904328946a7a---------------------

>P1;d1v66a-
----a1a69503a00560648104500251a6a377949700620261086a07760363023047769----

>P1;d1zrja1
------------741771769505530875846287a376007307624------------------------

>P1;d4uzwa1
------------98157275b703830794c274b4b494016303744578------------778aab79e


Translating the sequences
************C*HHHCCHHHHHHHHHHCCCCCCCCHHHHHHHHHHHH*C----------------------
----------------*CCHHHHHHHHHHCCCCCCC---***********C*---------------------
----**********H**CCHHHHHHHHHHCCCCCCCCHHHHHHHHHHHH*C******************----
------------C*HHHCCHHHHHHHHHH*CCCCCCCHHHHHHHHHHH*------------------------
------------C*HHHCCHHHHHHHHHH*CCCCCCCHHHHHHHHHHHH***------------*********

68906.tem
_________________________________
------------C*HHHCCHHHHHHHHHHCCCCCCCCHHHHHHHHHHHH*C*---------------------




Structural block scores
0	11	-	4.0	M	  5.5  75.0  28.8  75.0  75.0

14	16	H	4.1	M	  4.3  53.8  3.7  5.0  4.3

17	18	C	5.0	H	  3.5  6.5  3.0  4.0  4.5

19	28	H	5.0	H	  3.5  4.1  2.9  4.8  5.3

29	36	C	4.8	H	  5.8  15.2  6.8  6.3  7.1

37	48	H	4.4	M	  3.2  16.7  3.1  3.8  3.8

52	72	-	4.3	M	  75.0  75.0  17.6  75.0  46.9

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