Reading input alignment file to find conserved blocks of secondary structure

The input structure based alignment from Comparer
_____________________________________________

>P1;d1fx3a-
CEEEEEEEEEEEEEEECCCHHHHCCC-CCCCCEEEEEEEEEC------CEEEEEEEEEECCCCCCCCCCCEEEEEEEEEEEEECCC---HHHHHHHHHCHHHHHHHHHHHHHHHHHHHHC-CCCCCCCCCCCHHHHHHHHHCCCC

>P1;d2hnga1
-CEEECCCEEEEEEEEECCHHHHHHHCCCCCCCEEEEEEEEEECCCCEEEEEEEEEEEECC-------CEEEEEEEEEEEEEECCCCCCHHHCCHHHHHHHHHHHHC-CHHHHHHHHHHHHCCCCCCCCC---------------
PSA

>P1;d1fx3a-
76262482334635171332870464-35737161617556b------53110002040404894752002050400020203a1a---b752220210300640045037102520874-804717097280753276439598

>P1;d2hnga1
-8162594744515268185960984a53948251606237237a862010203040012a-------70204030102021364107618708b933660031016-0274034304843a78036074---------------


Translating the sequences
*EEEEEEEEEEEEEEE*CCHHHH***-CCCCCEEEEEEEEE*------*EEEEEEEEEECC*******C*EEEEEEEEEEEEECCC---HHHHHHHHH*HHHHHHHH*HHHHHHHHHHH*-CCCCCCCCC***************
-*EEE***EEEEEEEEECCHHHHHHH*CCCCC*EEEEEEEEE******EEEEEEEEEEECC-------CEEEEEEEEEEEEEECCC***HHH**HHHHHHHHHHHH*-*HHHHHHHHHHH*CCCCCCCCC---------------

54611.tem
_________________________________
-EEEEEEEEEEEEEEEECCHHHHHHH-CCCCCEEEEEEEEEE------EEEEEEEEEEECC-------CEEEEEEEEEEEEEECCC---HHHHHHHHHHHHHHHHHH-HHHHHHHHHHHH-CCCCCCCCC---------------




Structural block scores
1	16	E	4.4	M	  3.9  4.8

17	18	C	5.0	H	  3.0  4.5

19	25	H	4.1	M	  4.4  5.9

27	31	C	5.0	H	  5.0  5.8

32	41	E	4.6	H	  5.0  3.4

42	47	-	3.0	P	  75.0  6.1

48	58	E	4.8	H	  1.5  1.0

59	60	C	5.0	H	  2.0  6.2

61	67	-	3.0	P	  5.6  75.0

69	82	E	4.9	H	  1.3  1.3

83	85	C	5.0	H	  7.3  3.7

86	88	-	3.0	P	  75.0  4.3

89	106	H	4.6	H	  2.8  4.1

108	119	H	4.7	H	  3.2  3.2

121	129	C	5.0	H	  4.8  5.1

130	144	-	3.0	P	  5.2  75.0

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