Reading input alignment file to find conserved blocks of secondary structure

The input structure based alignment from Comparer
_____________________________________________

>P1;d1diva1
CHHHHHHHHHHHHHHHHCCC-CEEEEECCCHHHEEEEEECHHHHHHHHHHHHCCCCCHHHCCCC-CCEEECEEEEEEEEEECCEEEEEEEEEEECC

>P1;d2qamh1
---CCCCCCCCCHHHHCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHCCCC-CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC-
PSA

>P1;d1diva1
9b985736615523850361-4040414067c5506a20326401710674291806373051a-b213527547040402770305040204556

>P1;d2qamh1
---9995984542365149186061313169aa505660968300640459-c69164722218aa29474a918010305a934050405065a-


Translating the sequences
***HHHHHHHHHHHHHHCCC-CEEEEECCCHHHEEEEEECHHHHHHHHHHH*CCCCCHHHCCCC-CCEEECEEEEEEEEEECCEEEEEEEEEEEC*
---*********HHHH*CCC*C*****CCC*********CHHHHHHH****-CCCCC***CCCC*CC***C**********CC***********C-

55653.tem
_________________________________
---HHHHHHHHHHHHHHCCC-CEEEEECCCHHHEEEEEECHHHHHHHHHHH-CCCCCHHHCCCC-CCEEECEEEEEEEEEECCEEEEEEEEEEEC-




Structural block scores
0	2	-	3.0	P	  9.8  75.0

3	16	H	3.6	M	  4.6  5.6

17	19	C	5.0	H	  3.3  4.7

22	26	E	3.0	P	  1.8  2.2

27	29	C	5.0	H	  3.3  3.3

30	32	H	3.0	P	  8.2  10.0

33	38	E	3.0	P	  3.9  3.7

40	50	H	4.3	M	  3.5  4.1

52	56	C	5.0	H	  4.8  6.9

57	59	H	3.0	P	  4.3  4.3

60	63	C	5.0	H	  4.1  3.2

65	66	C	5.0	H	  6.8  6.2

67	69	E	3.0	P	  3.0  6.7

71	80	E	3.0	P	  3.3  3.8

81	82	C	5.0	H	  7.0  9.8

83	93	E	3.0	P	  2.1  2.9

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