Reading input alignment file to find conserved blocks of secondary structure

The input structure based alignment from Comparer
_____________________________________________

>P1;d1a62a1
--------CHHHHHCCCHHHHHHHHHCCCCCCCC--CHHHHHHHHHHHHHHCCC----

>P1;d2hjqa1
CCCCCCCCCHHHHCCCCHHHHHHHHHHHCCCCCCCCCHHHHHHHHHHHHHCCCC----

>P1;d2outa1
-----------------CHHHHHHHHCCCCCCCCCCCCHHHHHHHC---CCCCCCCCC
PSA

>P1;d1a62a1
--------7587169264960265058a287077--8377008413746676a6----

>P1;d2hjqa1
d9864153735605b39674037003638680982995841152047237a7aa----

>P1;d2outa1
-----------------68914660684b2938c709656067416---95ba6999a


Translating the sequences
--------CHHHH*CCCHHHHHHHHHCCCCCCCC--CHHHHHHHHHHHHH*CCC----
********CHHHH*CCCHHHHHHHHH**CCCCCCCCCHHHHHHHHHHHHHCCCC----
-----------------*HHHHHHHHCCCCCCCCCCC*HHHHHHH*---*CCCC****

68912.tem
_________________________________
--------CHHHH*CCCHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHHHCCCC----




Structural block scores
0	7	-	4.0	M	  75.0  6.2  75.0

9	12	H	4.0	M	  5.2  3.5  75.0

14	16	C	4.0	M	  5.7  7.8  75.0

17	25	H	4.9	H	  4.1  3.3  5.1

26	36	C	4.6	H	  18.9  6.2  6.7

37	49	H	4.5	M	  4.3  3.8  21.2

50	53	C	4.8	H	  7.4  9.6  8.2

54	57	-	4.0	M	  75.0  75.0  9.4

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