Reading input alignment file to find conserved blocks of secondary structure

The input structure based alignment from Comparer
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>P1;d1e8ca1
----CCHHHHHCCCCCCCC--CCCCCC-CCCHHHCCCCCEEEECCCCCCCHHHHHHHHHHCCCCEEEEECCCCCCCCCEECCCCCEEEECCHHHHHHHHHHHHCC-C

>P1;d4cvka1
CCCCEEHHHCHHHHCCEEECCCCEECEEECCCCCCCCCEEEECCCCC-CCHHHHHHHHHHCCCCEEEEC-------CCCCCC-CCEEEC-CHHHHHHHHHHHHHHHC
PSA

>P1;d1e8ca1
----230550053307703--449077-354087087400010147a96131841660184702000000795095231459b1000004806822a70652067-8

>P1;d4cvka1
14551404703a40906129a3240652134078047520000254a-823063094018470200003-------543b04-020020-607704a50a5236738


Translating the sequences
----**HHHHH***CC***--CC**C*-*CCHHHCCCC*EEEECCCC*CCHHHHHHHHHHCCCCEEEEE*******CCEECC*CCEEEE*CHHHHHHHHHHHH**-C
****EEHHH*HHHHCCEEE**CCEECE*ECC***CCCCEEEE*CCCC-CCHHHHHHHHHHCCCCEEEE*-------CC**CC-CCEEE*-CHHHHHHHHHHHHHH*C

63418.tem
_________________________________
----EEHHHHHHHHCCEEE--CCEECE-ECCHHHCCCCEEEEECCCC-CCHHHHHHHHHHCCCCEEEEE-------CCEECC-CCEEEE-CHHHHHHHHHHHHHH-C




Structural block scores
0	3	-	3.0	P	  75.0  3.8

4	5	E	3.0	P	  2.5  2.5

6	13	H	4.0	M	  2.6  3.6

14	15	C	5.0	H	  3.5  4.5

16	18	E	3.0	P	  3.3  3.0

19	20	-	3.0	P	  75.0  9.8

21	22	C	5.0	H	  4.0  2.5

23	24	E	3.0	P	  4.5  2.0

29	30	C	5.0	H	  4.5  3.5

31	33	H	3.0	P	  5.0  5.0

34	37	C	5.0	H	  4.8  4.0

38	42	E	4.2	M	  0.2  0.4

43	46	C	5.0	H	  5.6  5.4

48	49	C	5.0	H	  3.5  5.0

50	59	H	5.0	H	  3.8  3.4

60	63	C	5.0	H	  3.2  3.2

64	68	E	4.6	H	  0.0  0.6

69	75	-	3.0	P	  5.0  75.0

76	77	C	5.0	H	  2.5  4.5

78	79	E	3.0	P	  2.5  7.2

80	81	C	5.0	H	  7.0  2.0

83	84	C	5.0	H	  0.5  1.0

85	88	E	4.5	M	  0.0  0.5

91	104	H	4.7	H	  4.4  4.8

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