Reading input alignment file to find conserved blocks of secondary structure

The input structure based alignment from Comparer
_____________________________________________

>P1;d1olza3
---CHHH-CC-CHHHHHHCCCCCEEEECCCC------EEEECC---CCCCCHHHCCCCCCCCHHHCCCCC

>P1;d1txvb4
CCCCCCCCCCCCHHHHHCC-CCCEEEECCCCCCCCCCCEEEHHHHHHCCCCHHHEECC------------
PSA

>P1;d1olza3
---a098-3a-30260053535800102567------60142a---81a139a70223470618405895

>P1;d1txvb4
a725036718753950380-296001061a907ac3420014820475a037a40535------------


Translating the sequences
---CHHH-CC-CHHHHHHC*CCCEEEECCCC------EEEE**---*CCCCHHH**CC************
***C****CC*CHHHHH*C-CCCEEEECCCC*******EEEHH***HCCCCHHHEECC------------

103575.tem
_________________________________
---CHHH-CC-CHHHHHHC-CCCEEEECCCC------EEEEHH---HCCCCHHHEECC------------




Structural block scores
0	2	-	3.0	P	  75.0  6.5

4	6	H	3.0	P	  5.7  3.0

8	9	C	5.0	H	  6.8  4.5

12	17	H	4.7	H	  2.2  4.7

20	22	C	5.0	H	  5.3  5.7

23	26	E	5.0	H	  0.2  0.2

27	30	C	5.0	H	  5.0  6.6

31	36	-	3.0	P	  75.0  6.2

37	40	E	4.5	M	  2.8  0.8

41	42	H	3.0	P	  6.2  6.0

43	45	-	3.0	P	  75.0  2.0

47	50	C	5.0	H	  3.9  4.6

51	53	H	5.0	H	  8.8  7.2

54	55	E	3.0	P	  1.0  2.5

56	57	C	5.0	H	  2.5  4.0

58	69	-	3.0	P	  4.8  75.0

>>>>>>