Reading input alignment file to find conserved blocks of secondary structure

The input structure based alignment from Comparer
_____________________________________________

>P1;d3proc1
CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHEEEEEEEECCCCCEEEEEEECCC----CCCCC--------CEEEEECC---

>P1;d3proc2
------------------CCCCHHHHHHHHHHHCC---CCCEEEEEEE--HHHC-EEEEEEECCCHHHHHHHHHHHCCCCCCEEEEEECCCC
PSA

>P1;d3proc1
a8484246556064a32651580473174347405830895136142423b834120000135a----a092b--------9051663a---

>P1;d3proc2
------------------3876057026506831a---3b20041412--6a35-10002026a25a3068018509069710424417c77


Translating the sequences
******************HHHHHHHHHHHHHHHHH***HHHEEEEEEE*****C*EEEEEE*CC----*****--------CEEEEE*C---
------------------****HHHHHHHHHHH**---***EEEEEEE--HHHC-EEEEEEECC****HHHHH********CEEEEEEC***

54806.tem
_________________________________
------------------HHHHHHHHHHHHHHHHH---HHHEEEEEEE--HHHC-EEEEEEECC----HHHHH--------CEEEEEEC---




Structural block scores
0	17	-	3.0	P	  5.2  75.0

18	34	H	4.3	M	  4.0  4.6

35	37	-	3.0	P	  3.7  75.0

38	40	H	3.0	P	  7.3  5.5

41	47	E	5.0	H	  3.0  1.7

48	49	-	3.0	P	  2.5  75.0

50	52	H	3.0	P	  7.5  6.5

55	61	E	4.7	H	  0.9  0.7

62	63	C	5.0	H	  7.8  8.2

64	67	-	3.0	P	  75.0  5.1

68	72	H	3.0	P	  6.6  3.0

73	80	-	3.0	P	  75.0  5.5

82	87	E	4.7	H	  3.5  2.5

89	91	-	3.0	P	  75.0  8.8

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