Reading input alignment file to find conserved blocks of secondary structure

The input structure based alignment from Comparer
_____________________________________________

>P1;d4adya3
CCCCEEEEECCCCCEECCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHCCCCCCCEEECCCCCCCEEEEEEECCCCCCCCEECCCCC

>P1;d4cr2z3
-CCCCEEECC-CCCCCCCCCCCC-----------CCCCCCCCCCCC----CCCCC---CCCCCCCCC-CEEECCCC-HHHCCCC------
PSA

>P1;d4adya3
a83204021495812051510307a307796639912426072035900720513b3104149a17929515060436768174472b84

>P1;d4cr2z3
-a45040115-87540506083c-----------982606144605----94506---570884665-54060518-7796732------


Translating the sequences
*CCCEEEEEC*CCCEECCCCCCC***********CCCCCCCCCCCC****HCCCC***EEECCCCCC*EEEEEEEC****CCCE******
-CCC*EEE*C-CCC**CCCCCCC-----------CCCCCCCCCCCC----*CCCC---***CCCCCC-*EEE***C-HHHCCC*------

345918.tem
_________________________________
-CCCEEEEEC-CCCEECCCCCCC-----------CCCCCCCCCCCC----HCCCC---EEECCCCCC-EEEEEEEC-HHHCCCE------




Structural block scores
1	3	C	5.0	H	  4.3  6.5

4	8	E	4.2	M	  1.4  1.2

11	13	C	5.0	H	  4.7  6.7

14	15	E	3.0	P	  1.0  2.0

16	22	C	5.0	H	  2.1  4.9

23	33	-	3.0	P	  6.1  75.0

34	45	C	5.0	H	  3.4  4.2

46	49	-	3.0	P	  4.0  75.0

51	54	C	5.0	H	  2.2  3.8

55	57	-	3.0	P	  5.2  75.0

58	60	E	3.0	P	  1.7  4.0

61	66	C	5.0	H	  6.8  6.2

68	74	E	3.9	M	  3.7  3.0

77	79	H	3.0	P	  6.3  7.7

80	82	C	5.0	H	  5.3  5.3

84	89	-	3.0	P	  6.1  75.0

>>>>>>