Reading input alignment file to find conserved blocks of secondary structure

The input structure based alignment from Comparer
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>P1;d1kl9a1
CCC-CHHHHHHHHHHC-CHHHHC-CHHHHCCCCCCHHHHHHHCHHHHHHHHCCCCHHHHHHC-CCCC-CHHHHCCCCCC----CCCHHHHHHHC----

>P1;d2a19a2
CCHHHHHHHHHHHHHHHHHHHHHHHHHHHCCC--CHHHHHHHCHHHHHHHHC----CHHHHHHHHHH-CHHHHCCCCCCCHHHHHHHHHHHCC-----

>P1;d3cw2c2
CCCCHHHHHHHHHHHHHHHHHHHHHHHHHCCC--CHHHHHHHCHHHHHCCCC----CHHHHHHHHHHHCCHHHHCCCCCC-CCHHHHHHHHHHHHHHC
PSA

>P1;d1kl9a1
769-648787549824-307600-601861919b6376016200440185485722003600-6058-45620880919----91106800573----

>P1;d2a19a2
77976777866865356404510550075283--72740253006303973a----20330066058-587008b0a1268701520393067-----

>P1;d3cw2c2
a77847666762653352036003500843a1--65850254005405817b----401600430186867105607049-81162018006643965


Translating the sequences
CCC-*HHHHHHHHHH*-*HHHH*-*HHHHCCC**CHHHHHHHCHHHHHHHHC*****HHHH*-****-CHHHHCCCCCC----***HHHHHHH*----
CC**HHHHHHHHHHHHHHHHHHHHHHHHHCCC--CHHHHHHHCHHHHHHHHC----CHHHHHHHHHH-CHHHHCCCCCCC***HHHHHHHH**-----
CCC*HHHHHHHHHHHHHHHHHHHHHHHHHCCC--CHHHHHHHCHHHHH***C----CHHHHHHHHHH*C*HHH*CCCCCC-**HHHHHHHHHH*****

116742.tem
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CCC*HHHHHHHHHHHHHHHHHHHHHHHHHCCC--CHHHHHHHCHHHHHHHHC----CHHHHHHHHHH-CHHHHCCCCCCC-**HHHHHHHHHH*----




Structural block scores
0	2	C	4.7	H	  7.3  7.7  8.2

4	28	H	4.7	H	  10.4  4.6  3.9

29	31	C	5.0	H	  3.7  4.3  4.8

32	33	-	4.0	M	  10.2  75.0  75.0

35	41	H	5.0	H	  3.6  3.3  4.1

43	50	H	4.6	H	  3.2  3.9  3.8

52	55	-	4.0	M	  4.0  75.0  75.0

57	66	H	4.4	M	  10.3  3.1  2.3

69	72	H	4.8	H	  3.2  3.8  3.5

73	79	C	4.7	H	  15.7  5.6  4.4

81	82	*	2.7	P	  75.0  3.5  4.5

83	92	H	4.5	M	  3.7  3.6  3.0

94	97	-	4.0	M	  75.0  75.0  5.8

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