Reading input alignment file to find conserved blocks of secondary structure

The input structure based alignment from Comparer
_____________________________________________

>P1;d1kp8a3
-CCCCHHHHHHHHHHHCC------CCHHHHHHHHHHHHHHC----CCCE-----EEEECCCCC---CCEEEEECHHHHHHHCEEEEECCCCCHHHHHHHHHHHHHHHHHHHHHHHC-

>P1;d1q3qa3
CCCCCHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHCEECCCCEECCHHHEEEEEEECCCHHHCEEE----------CCEEEEEEECCHHHHHHHHHHHHHHHHHHHHHHHCC
PSA

>P1;d1kp8a3
-a078682036302820a------82850070015008509----4747-----050540856---9141536aa988988530102001688a6157226304801950363059-

>P1;d1q3qa3
482446730374039204a3804924a20050005002600756777160629306143628660650517----------671303020848940430260045006302620281


Translating the sequences
-CCCCHHHHHHHHHHHCC------**HHHHHHHHHHHHHHC----CC*E-----EEEE***CC---*CEEE**********CEEEEE***CCHHHHHHHHHHHHHHHHHHHHHHHC-
*CCCCHHHHHHHHHHHCC******HHHHHHHHHHHHHHHHC****CCEE*****EEEEEEECC***HCEEE----------C*EEEEEEECCHHHHHHHHHHHHHHHHHHHHHHHC*

54849.tem
_________________________________
-CCCCHHHHHHHHHHHCC------HHHHHHHHHHHHHHHHC----CCEE-----EEEEEEECC---HCEEE----------CEEEEEEEECCHHHHHHHHHHHHHHHHHHHHHHHC-




Structural block scores
1	4	C	5.0	H	  6.4  4.5

5	15	H	5.0	H	  3.6  4.0

16	17	C	5.0	H	  5.2  2.0

18	23	-	3.0	P	  75.0  5.8

24	39	H	4.8	H	  3.1  2.3

41	44	-	3.0	P	  75.0  6.2

45	46	C	5.0	H	  5.5  7.0

47	48	E	4.0	M	  5.5  3.5

49	53	-	3.0	P	  75.0  4.0

54	60	E	4.1	M	  3.1  3.1

61	62	C	5.0	H	  5.5  7.0

63	65	-	3.0	P	  75.0  4.0

68	70	E	5.0	H	  3.3  4.3

71	80	-	3.0	P	  8.0  75.0

82	89	E	4.0	M	  0.9  2.0

90	91	C	5.0	H	  7.0  6.0

92	114	H	5.0	H	  4.1  2.9

>>>>>>