Reading input alignment file to find conserved blocks of secondary structure

The input structure based alignment from Comparer
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>P1;d1xkpa1
CCCHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHCCCCCCCCCCCCCCCCCC---CHHHHCCHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHCCCCHHHHHHHHCCCCCCCHHHHHHHHCCHHHHHHHCCCCCCCCCHHHHHHHCCCC

>P1;d1xl3c1
CCCHHHHHHHHHHHHC-----------------------CCCCHHHHHHHHHCCCCCCCCCCHHHHHCCCHHHCCHHHCCCHHHHHHHHHHHH------HHHHHHHHHHHHHHHCC-----------------------------------------------------------------------C

>P1;d1z21a1
-----CHHHHHHHHHHHHHHCC---------------------CCCHHHHHHHH---HHHHHHHHHHHCCCCC----CCCHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHCCC---HHHHHHHHHHHHHHC--------------------------------------------------------
PSA

>P1;d1xkpa1
a573973165028407732817573862861183049218a164a406306927---010300001702730d4870770370054004300274062011001011303621678705322003000502381853a4027505306b0519300810200562278495a94491680282070a5

>P1;d1xl3c1
b179962673077018-----------------------7616286027008239272464161046074078277b4056671162017105------4016404743786777a-----------------------------------------------------------------------9

>P1;d1z21a1
-----8a988157206713739---------------------85579204600---430173048402b49b----a064a70044036006620876730420061027511---800350063018509--------------------------------------------------------


Translating the sequences
CCCHHHHHHHHHHHHHHHH*CC*****************CCCCCCC******CC---CHHHH**HHHH**HCCC*HHH**HHHHHHHHHHHHHHH****HHHHHHHHHHHHHHCCC***HHHHHHHHHHHH********************************************************C
CCCHHHHHHHHHHHH*-----------------------CCCC***HHHHHHCC***C****HHHHH*CCH**C*HHHCC*HHHHHHHHHHHH------HHHHHHHHHHHHHH*CC-----------------------------------------------------------------------C
-----*HHHHHHHHHHHHH*CC---------------------CCCHHHHHH**---*HHHHHHHHHHCC*CC----*CCHHHHHHHHHHHHHHH****HHHHHHHHHHHH**C---**HHHHHHHHHHHH*--------------------------------------------------------

140591.tem
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CCCHHHHHHHHHHHHHHHH*CC-----------------CCCCCCCHHHHHHCC---CHHHHHHHHHHCCHCCC*HHHCCHHHHHHHHHHHHHHH****HHHHHHHHHHHHHHCCC-**HHHHHHHHHHHH*-------------------------------------------------------C




Structural block scores
0	2	C	4.0	M	  7.5  6.5  75.0

3	18	H	4.6	H	  4.2  18.1  14.1

20	21	C	4.0	M	  4.0  75.0  6.0

22	38	-	4.0	M	  4.4  75.0  75.0

39	45	C	4.0	M	  6.3  5.1  45.4

46	51	H	4.0	M	  4.0  2.8  4.7

52	53	C	4.0	M	  4.5  2.5  0.0

54	56	-	4.0	M	  75.0  6.0  75.0

58	67	H	4.3	M	  1.2  3.2  3.0

68	69	C	4.0	M	  4.5  5.5  6.8

71	73	C	4.0	M	  5.8  5.7  31.8

75	77	H	4.0	M	  4.7  7.5  53.5

78	79	C	4.0	M	  3.5  2.5  3.0

80	94	H	4.8	H	  2.6  12.9  3.5

95	98	*	2.7	P	  2.0  75.0  5.2

99	112	H	4.9	H	  1.4  4.4  2.7

113	115	C	4.0	M	  7.0  8.2  50.3

117	118	*	2.7	P	  2.5  75.0  4.0

119	130	H	4.0	M	  1.4  75.0  2.6

132	186	-	4.0	M	  4.3  75.0  75.0

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