Reading input alignment file to find conserved blocks of secondary structure

The input structure based alignment from Comparer
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>P1;d1utaa-
----CCCCCCCCCCCCCCCHHHHHHHHHHHHHHCCCCEEEEECCEEEEECCCCCCCHHHHHHHHHHHHHCCCCCCCCCCCC

>P1;d1x60a-
CCCCCCCCCEEEEEEEECCHHHHHHHHHHHHHHCCCEEEEEECCEEEEEEEEECCHHHHHHHHHHHHHHCCC-CEEEECC-
PSA

>P1;d1utaa-
----a587524020000636a7077036302919080737857b41202177163497056029406508084050363af

>P1;d1x60a-
c9a986a062102041477577058206307747091617439842202002494584068107605c0918-0616456-


Translating the sequences
----CCCCC********CCHHHHHHHHHHHHHHCCC*EEEEECCEEEEE****CC*HHHHHHHHHHHHHCCC*C****CC*
****CCCCCEEEEEEEECCHHHHHHHHHHHHHHCCCEEEEEECCEEEEEEEEECCHHHHHHHHHHHHHHCCC-CEEEECC-

110997.tem
_________________________________
----CCCCCEEEEEEEECCHHHHHHHHHHHHHHCCCEEEEEECCEEEEEEEEECCHHHHHHHHHHHHHHCCC-CEEEECC-




Structural block scores
0	3	-	3.0	P	  75.0  10.2

4	8	C	5.0	H	  7.1  6.1

9	16	E	3.0	P	  1.0  1.8

17	18	C	5.0	H	  4.5  7.0

19	32	H	5.0	H	  4.4  4.4

33	35	C	5.0	H	  5.7  5.3

36	41	E	4.7	H	  5.0  3.7

42	43	C	5.0	H	  9.2  8.5

44	52	E	4.1	M	  2.8  1.8

53	54	C	5.0	H	  4.5  6.5

55	68	H	4.9	H	  4.1  4.5

69	71	C	5.0	H	  5.3  6.0

74	77	E	3.0	P	  3.5  4.2

78	79	C	5.0	H	  6.8  5.5

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