Reading input alignment file to find conserved blocks of secondary structure

The input structure based alignment from Comparer
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>P1;d3ci0k1
CCEECCCCC----------HHHC-HHHHHHC-----CCHHHHCCCC------------------------------CCCCCHHHHHCCHHHCCCCHHHHHHHHHHEECC----

>P1;d3ci0k2
CCEEHHHHHCCCCCCCCHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHCCCCCCCCCCCCCHHHHHCCCCCCCCCCCCCCCHHHHHHCCCC---CHHHHHHHCCCEECCCCCC
PSA

>P1;d3ci0k1
672302706----------3960-8406821-----766005714a------------------------------a009616600818408b278812760572002a----

>P1;d3ci0k2
b32000200583a7b417107501720481a0796301200000000019688440710402810473b9547021740862630430140---68b0176056402058448


Translating the sequences
CCEE*****----------HHH*-HHHHHHC-----**HHHH****------------------------------CCCCCHHHHH*CHHH***CHHHHHHHHHHEECC----
CCEEHHHHH**********HHHH*HHHH**C*****HHHHHHHHHH******************************CCCCCHHHHHHC***---CHHHHHHH***EECC****

158544.tem
_________________________________
CCEEHHHHH----------HHHH-HHHHHHC-----HHHHHHHHHH------------------------------CCCCCHHHHHHCHHH---CHHHHHHHHHHEECC----




Structural block scores
0	1	C	5.0	H	  6.5  7.2

2	3	E	5.0	H	  2.5  1.0

4	8	H	3.0	P	  3.0  0.4

9	18	-	3.0	P	  75.0  5.8

19	22	H	4.5	M	  4.5  3.0

24	29	H	4.3	M	  4.7  3.7

31	35	-	3.0	P	  75.0  5.0

36	45	H	3.8	M	  4.7  0.3

46	75	-	3.0	P	  75.0  3.9

76	80	C	5.0	H	  5.1  5.0

81	86	H	4.7	H	  3.5  3.0

88	90	H	3.0	P	  4.0  1.7

91	93	-	3.0	P	  7.2  75.0

95	104	H	4.4	M	  4.6  4.8

105	106	E	5.0	H	  0.0  1.0

107	108	C	5.0	H	  6.2  2.5

109	112	-	3.0	P	  75.0  6.0

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