Reading input alignment file to find conserved blocks of secondary structure

The input structure based alignment from Comparer
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>P1;d1puza-
CCCCCHHHHHHHHHCCCCCCHHHHHHHHHHHHHCHHHCCHHHHHHHHHHHCCCHHHHHHHHHCCCCCCCCCHHHHHHHHHHC---------

>P1;d1x6ia1
---CCCCCHHHHHHHCCCCCHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHCCCHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHHCCCCC
PSA

>P1;d1puza-
99735a9137604640684596046307701661269067920610440063a08402102788291b57808421730471---------

>P1;d1x6ia1
---271865950473061a385037201300561076076831510040072827503410578b60a49602400620343276259a8d


Translating the sequences
***CCHHHHHHHHH*CCCCCHHHHHHHHHHHHH*HHHCCHHHHHHHHHHHCCCHHHHHHHHHCCCCCCC**HHHHHHHHHH*---------
---CC***HHHHHHHCCCCCHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHCCCHHHHHHHH*CCCCCCCHHHHHHHHHHHHH*********

109910.tem
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---CCHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHCCCHHHHHHHHHCCCCCCCHHHHHHHHHHHHH---------




Structural block scores
0	2	-	3.0	P	  8.3  75.0

3	4	C	5.0	H	  4.0  4.5

5	14	H	4.2	M	  5.0  4.8

15	19	C	5.0	H	  4.6  4.1

20	36	H	4.9	H	  4.3  3.2

37	38	C	5.0	H	  3.0  3.5

39	49	H	5.0	H	  3.0  2.5

50	52	C	5.0	H	  6.5  5.7

53	61	H	4.8	H	  2.7  3.0

62	68	C	5.0	H	  6.4  6.7

69	81	H	4.5	M	  4.0  3.0

82	90	-	3.0	P	  75.0  7.0

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