Reading input alignment file to find conserved blocks of secondary structure

The input structure based alignment from Comparer
_____________________________________________

>P1;d3fkea-
-CCCHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHCCCHHHHHHHHHHHCHHHCCCCCCEEEECCHHHCCHHHHHHEECCCC-CCCHHHCEEEEEEECCCCEEEEEC

>P1;d6dkua-
CCCCHHHHHHHHHHCCCCCCCHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHCHHHHCCCCCEEECCCHHHCCHHHHHHCEECCCCCCCCCCCEEEEEEEC-CEEEEEEC
PSA

>P1;d3fkea-
-b261760373029406a8331201004000630654b11950352047017893623400330054063058360353718759504a403a2048229-813018110010308787320023

>P1;d6dkua-
a716594036302950a8965021000200041067480054005005602879570540042005617404616014481955860499028206914a8813015400000306-a7320042


Translating the sequences
-CCCHHHHHHHHH*CCCCCCCHHHHHHHHHHHHHHH***HHHHHHHHHHHHHHCCCHHHHHHHHHHHCHHH*CCCCCEEEECCHHHCCHHHHHHEE*CCC-CCCHHHCEEEEEEEC*C*EEEEEC
*CCCHHHHHHHHHHCCCCCCCHHHHHHHHHHHH***HHHHHHHHHHHHHHHH*CCCHHHHHHHHHHHCHHHHCCCCCEEE*CCHHHCCHHHHHH*EECCC*CCC***CEEEEEEEC-CEEEEEEC

267597.tem
_________________________________
-CCCHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHCHHHHCCCCCEEEECCHHHCCHHHHHHEEECCC-CCCHHHCEEEEEEEC-CEEEEEEC




Structural block scores
1	3	C	5.0	H	  6.5  4.7

4	13	H	4.8	H	  3.8  4.1

14	20	C	5.0	H	  4.9  6.2

21	52	H	4.6	H	  3.0  2.4

53	55	C	5.0	H	  6.0  7.0

56	66	H	5.0	H	  2.2  2.4

68	71	H	4.5	M	  3.5  3.8

72	76	C	5.0	H	  4.0  2.8

77	80	E	4.5	M	  4.0  4.2

81	82	C	5.0	H	  7.5  7.0

83	85	H	5.0	H	  6.3  6.3

86	87	C	5.0	H	  2.0  2.0

88	93	H	5.0	H	  5.0  5.0

94	96	E	3.7	M	  4.0  5.0

97	99	C	5.0	H	  4.3  5.2

101	103	C	5.0	H	  4.0  4.0

104	106	H	3.0	P	  3.0  2.0

108	114	E	5.0	H	  0.7  0.4

118	123	E	4.7	H	  2.3  2.7

>>>>>>