Reading input alignment file to find conserved blocks of secondary structure

The input structure based alignment from Comparer
_____________________________________________

>P1;d1rqpa1
CCCEEECCEEEEEEEEEECCCCEEEEEEEHHHHHCCCCCCCCEEEEEECCCEEEEEEEECCHHHHCCCCCEEEEECCCCEEEEEECCCCCHHHHCCCCCCEEEEEC

>P1;d2q6ka2
-----------CCEEEECCCCCCEEEEEEHHHHC--------CEEEEECCCEEEEECCCCCHHHC-CCCCEEEEECCCCEEEEEECCCCHHHHCCCCCCCCCEEEC
PSA

>P1;d1rqpa1
991766c70021304302677000202025520681a0959390502059845271502554741a9726200010962400002173200445807681603032

>P1;d2q6ka2
-----------5405613977010204126861a--------5340403b724170230964751-a756100021996500000183203752507564807058


Translating the sequences
***********EEEEEEECCCCEEEEEEEHHHHH********EEEEEECCCEEEEEEEECCHHHH*CCCCEEEEECCCCEEEEEECCCC*HHHHCCCCCCEEEEEC
-----------**EEEE*CCCC*EEEEEEHHHH*--------*EEEEECCCEEEEE***CCHHH*-CCCCEEEEECCCCEEEEEECCCCHHHH*CCCCCC**EEEC

101852.tem
_________________________________
-----------EEEEEEECCCCEEEEEEEHHHHH--------EEEEEECCCEEEEEEEECCHHHH-CCCCEEEEECCCCEEEEEECCCCHHHHHCCCCCCEEEEEC




Structural block scores
0	10	-	3.0	P	  5.4  75.0

11	17	E	4.1	M	  1.9  3.4

18	21	C	5.0	H	  5.0  5.8

22	28	E	4.7	H	  0.9  1.4

29	33	H	4.6	H	  3.6  6.3

34	41	-	3.0	P	  5.7  75.0

42	47	E	4.7	H	  2.7  2.7

48	50	C	5.0	H	  7.3  7.2

51	58	E	4.2	M	  3.2  2.4

59	60	C	5.0	H	  5.0  7.5

61	64	H	4.5	M	  4.0  4.2

66	69	C	5.0	H	  6.0  7.1

70	74	E	5.0	H	  0.6  0.6

75	78	C	5.0	H	  4.2  6.2

79	84	E	5.0	H	  1.0  0.8

85	88	C	5.0	H	  3.2  3.5

89	93	H	4.2	M	  2.6  3.4

94	99	C	5.0	H	  5.0  4.5

100	104	E	4.2	M	  2.4  4.0

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