Reading input alignment file to find conserved blocks of secondary structure

The input structure based alignment from Comparer
_____________________________________________

>P1;d1vzia1
------CCCCCCCHHHHCEEEEEEC-------CEEEEEECC-CCCCCCCCCCEEEEEEEEC-------CEEEEEECCCC-------------CCCEEEEECCCC---CCEEEEEECCCEEEEEEC------

>P1;d3qzba1
CCHHHHEECCCCCCCCCCEEEECCCEECCCCEEEEEEEECCCCCCCCCCCCCEEEEEEEEEECCCCCCEEEEEEECCCCCCCCCCCCCCCCCCCCEEEEEEECCCCEEEEEEEEECCCEEEEEEEEEEECC
PSA

>P1;d1vzia1
------2484b1676403040583b-------a00204007-6703078821033010208-------b444257073b-------------561304070b19---703020303523304374------

>P1;d3qzba1
787766167553672300010504960756470603010035480414271004101021305c267454144240720042a845461a8347052414150662020201030154710334450505c


Translating the sequences
------**CCCCCHHHHCEEEEEEC-------*EEEEEECC-CCCCCCCCCCEEEEEEEE*-------*EEEEEECCCC-------------CCCEEEEE**CC---**EEEEEECCCEEEEEE*------
******EECCCCC****CEEEE**C*******EEEEEEECC*CCCCCCCCCCEEEEEEEEE*******EEEEEEECCCC*************CCCEEEEEEECC***EEEEEEEECCCEEEEEEE******

49367.tem
_________________________________
------EECCCCCHHHHCEEEEEEC-------EEEEEEECC-CCCCCCCCCCEEEEEEEEE-------EEEEEEECCCC-------------CCCEEEEEEECC---EEEEEEEECCCEEEEEEE------




Structural block scores
0	5	-	3.0	P	  75.0  6.8

6	7	E	3.0	P	  3.0  3.5

8	12	C	5.0	H	  6.1  5.2

13	16	H	3.0	P	  4.2  3.0

18	23	E	4.3	M	  3.3  1.7

25	31	-	3.0	P	  75.0  5.0

32	38	E	4.7	H	  2.4  1.4

39	40	C	5.0	H	  3.5  1.5

42	51	C	5.0	H	  4.2  3.1

52	60	E	4.8	H	  1.9  1.3

61	67	-	3.0	P	  75.0  5.2

68	74	E	4.7	H	  5.4  3.4

75	78	C	5.0	H	  5.4  2.2

79	91	-	3.0	P	  75.0  5.1

92	94	C	5.0	H	  4.0  3.7

95	101	E	4.4	M	  3.6  3.1

102	103	C	5.0	H	  5.0  3.0

104	106	-	3.0	P	  75.0  2.7

107	114	E	4.5	M	  1.9  1.0

115	117	C	5.0	H	  3.3  3.3

118	124	E	4.7	H	  3.4  3.1

125	130	-	3.0	P	  75.0  4.6

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