Reading input alignment file to find conserved blocks of secondary structure

The input structure based alignment from Comparer
_____________________________________________

>P1;d2bska1
------CCHHHHHHHHHHHHHHHC-CCCCCCCCCHHHHHHHHHHHHHH--CCHHHHHHHHHHHHCCCCCCCCCC

>P1;d2bskb1
------CCCCCCCC-CHHHHHHHCCCCCCCCCCC----CHHHHHHHHHCCHHHHHCCHHHHHCCCC--------

>P1;d3dxra-
------CCCCCHHHHHHHHHHHHC-CCCCCCCCC---HHHHHHHHHHH--HHHCCHHHHHHHHHCCCC------

>P1;d3dxrb-
CCCCCCCHHHHHHHHHHHHHHHCC-CCCCCCCCC----CHHHHHHHHH--HHHHHHHHHHHHHC-C--------
PSA

>P1;d2bska1
------975c56880775167701-74677a97489154448725892--554876764785657698779a89

>P1;d2bskb1
------9a877987-774157701578686ba55----a35543882684778787966884567a--------

>P1;d3dxra-
------bbaa38781684066500-a5686a946---a9065438813--89256388675577689a------

>P1;d3dxrb-
bb9898888627551685078709-77b49d967----b255438814--78268658768778-9--------


Translating the sequences
------CC***HHHHHHHHHHHHC-CCCCCCCCC*****HHHHHHHHH--**HHHHHHHHHHH*CC********
------CC******-*HHHHHHHC*CCCCCCCCC----*HHHHHHHHH**HHHHH**HHHHH**CC--------
------CC***HHHHHHHHHHHHC-CCCCCCCCC---**HHHHHHHHH--HHH**HHHHHHHH*CC**------
******C****HHHHHHHHHHH*C-CCCCCCCCC----*HHHHHHHHH--HHHHHHHHHHHHH*-C--------

144122.tem
_________________________________
------CC***HHHHHHHHHHHHC-CCCCCCCCC---**HHHHHHHHH--HHHHHHHHHHHHH*CC**------




Structural block scores
0	5	-	4.3	M	  75.0  75.0  75.0  9.5

6	7	C	4.7	H	  8.0  9.8  11.5  8.0

8	10	*	1.0	P	  7.5  7.3  8.0  5.3

11	22	H	4.6	H	  5.2  11.4  4.9  4.9

25	33	C	5.0	H	  6.8  7.4  7.2  8.2

34	36	-	4.3	M	  6.0  75.0  75.0  75.0

37	38	*	2.2	P	  4.5  42.8  9.8  43.2

39	47	H	5.0	H	  5.4  4.9  4.2  4.4

48	49	-	4.3	M	  75.0  6.0  75.0  75.0

50	62	H	4.6	H	  6.0  6.9  6.1  6.5

64	65	C	4.7	H	  6.5  8.8  7.0  42.0

66	67	*	3.5	M	  8.5  75.0  9.8  75.0

68	73	-	4.3	M	  8.4  75.0  75.0  75.0

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