Reading input alignment file to find conserved blocks of secondary structure

The input structure based alignment from Comparer
_____________________________________________

>P1;d1dqca-
CCCCCCCCCCCCCCCCEECCCCCCCCEEECCCCCCEEECCCCCCEEECCCCEEECHHHHCCCCCCCCCCCCCC

>P1;d1iyca-
----------------CCCCCCCCCCCCC------CCCCCCCCCCEEC--CEECCHHHHC-------------
PSA

>P1;d1dqca-
957182628000886525505300001040495605136057c12011856702559609090917247738a

>P1;d1iyca-
----------------8b71904867659------6911038b1647b--940224862a-------------


Translating the sequences
****************EECCCCCCCCEEE******EEECCCCCCEEEC**CEEECHHHHC*************
----------------**CCCCCCCC***------***CCCCCC*EEC--CEE*CHHHHC-------------

57625.tem
_________________________________
----------------EECCCCCCCCEEE------EEECCCCCCEEEC--CEEECHHHHC-------------




Structural block scores
0	15	-	3.0	P	  4.7  75.0

16	17	E	3.0	P	  3.5  9.8

18	25	C	5.0	H	  1.6  5.2

26	28	E	3.0	P	  1.7  6.7

29	34	-	3.0	P	  4.0  75.0

35	37	E	3.0	P	  3.0  5.3

38	43	C	5.0	H	  5.2  4.1

44	46	E	4.3	M	  1.0  5.7

48	49	-	3.0	P	  6.5  75.0

51	53	E	4.3	M	  3.0  2.0

55	58	H	5.0	H	  5.0  5.0

60	72	-	3.0	P	  5.2  75.0

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