Reading input alignment file to find conserved blocks of secondary structure

The input structure based alignment from Comparer
_____________________________________________

>P1;d1gd8a-
CHHHHHHHHHHHHHHHHHCEEEEEHHHHHHHHHHHHHHHHHHHHCC--HHHHHHHHHHCCCHHHHHHHHHCHHHHCCCCCCCCEEEEEEEEECCCCCCEEEEEEECC---------

>P1;d2cqma1
------CHHHHHHHHHHCCEEEEEHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHCCCCCHHHHHHHCHHHHHHHCCCCCEEEEECCCC-CCCCCCEEEEEECCCCCCCCCCC
PSA

>P1;d1gd8a-
b9a6364128003300574624302640640380024006001514--8604540462052670053006500340593a690041664b7649b663310101126---------

>P1;d2cqma1
------825a1024006533250359407604940260043015657598036104810747701440093004507a5c5a1061491646-897777300010309937818a6


Translating the sequences
******HHHHHHHHHHHHCEEEEEHHHHHHHHHHHHHHHHHHHHCC--HHHHHHHHHHCCCHHHHHHHHHCHHHH***CCCCCEEEEEEEEE*CCCCCEEEEEEECC---------
------*HHHHHHHHHH*CEEEEEHHHHHHHHHHHHHHHHHHHHCC**HHHHHHHHHHCCC**HHHHHHHCHHHHHHHCCCCCEEEEE****-CCCCC*EEEEEECC*********

64263.tem
_________________________________
------HHHHHHHHHHHHCEEEEEHHHHHHHHHHHHHHHHHHHHCC--HHHHHHHHHHCCCHHHHHHHHHCHHHHHHHCCCCCEEEEEEEEE-CCCCCEEEEEEECC---------




Structural block scores
0	5	-	3.0	P	  7.7  75.0

6	17	H	4.7	H	  2.8  3.6

19	23	E	5.0	H	  3.0  2.6

24	43	H	5.0	H	  2.5  3.5

44	45	C	5.0	H	  2.5  5.5

46	47	-	3.0	P	  75.0  6.0

48	57	H	5.0	H	  3.9  4.0

58	60	C	5.0	H	  2.3  3.7

61	69	H	4.6	H	  3.0  3.6

71	77	H	4.1	M	  3.0  3.8

78	82	C	5.0	H	  5.7  6.8

83	91	E	4.1	M	  5.1  4.1

93	97	C	5.0	H	  7.1  7.6

98	104	E	4.7	H	  1.0  1.6

105	106	C	5.0	H	  4.0  1.5

107	115	-	3.0	P	  75.0  6.8

>>>>>>