Reading input alignment file to find conserved blocks of secondary structure

The input structure based alignment from Comparer
_____________________________________________

>P1;d1nyna-
CCCCEEEEEECCCCEEEEEECCHHHHHHHHHCCCCCCHHHHCCCCCCEECCCCCCCCCCCEECCHHHHHHHCCCCCCHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCC

>P1;d1t95a2
C-CCEEEEEEECCEEEEEEEC-HHHHHHHHCCCCC-CHHHHCCCCCCEEECC------CCEECCHHHHHHHHCC-CCHHHHHHHHC-------------------------
PSA

>P1;d1nyna-
6aa333052819d640002024693086048a547a207700355502137a89a39ca21707a731290078c4845400240077045c79a67a8b899dabaa8af

>P1;d1t95a2
c-a252253639744010304-383152076a6a0-8186004463011309------8766086920681092-36137006600-------------------------


Translating the sequences
C*CCEEEEEE*CC*EEEEEEC*HHHHHHHHHCCCC*CHHHHCCCCCCEE*CC******CCEECCHHHHHHH*CC*CCHHHHHHHHH*************************
C-CCEEEEEEECCEEEEEEEC-HHHHHHHH*CCCC-CHHHHCCCCCCEEECC------CCEECCHHHHHHHHCC-CCHHHHHHHH*-------------------------

89895.tem
_________________________________
C-CCEEEEEEECCEEEEEEEC-HHHHHHHHHCCCC-CHHHHCCCCCCEEECC------CCEECCHHHHHHHHCC-CCHHHHHHHHH-------------------------




Structural block scores
2	3	C	5.0	H	  6.8  6.2

4	10	E	4.7	H	  3.1  3.7

11	12	C	5.0	H	  11.2  8.0

13	19	E	4.7	H	  1.7  1.7

22	30	H	4.8	H	  4.9  3.9

31	34	C	5.0	H	  6.6  6.8

37	40	H	5.0	H	  3.5  3.8

41	46	C	5.0	H	  3.0  2.8

47	49	E	4.3	M	  2.0  1.7

50	51	C	5.0	H	  8.8  4.5

52	57	-	3.0	P	  8.7  75.0

58	59	C	5.0	H	  6.2  7.5

60	61	E	5.0	H	  4.0  6.0

62	63	C	5.0	H	  3.5  4.0

64	71	H	4.8	H	  4.1  4.0

72	73	C	5.0	H	  7.5  5.5

75	76	C	5.0	H	  6.0  4.5

77	85	H	4.8	H	  2.1  2.6

86	110	-	3.0	P	  9.1  75.0

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