Reading input alignment file to find conserved blocks of secondary structure

The input structure based alignment from Comparer
_____________________________________________

>P1;d2i52a1
----CCCCHHHC-CCCHHHHHHHHHHHHHHHHHHHHCCCEECCCCHHHHHHHHHHHHCCCCCEEEEEEEECCCC-CCEECCCCCEEEEEEEEECCEEEEEEEEEECCCCEEEEEEEEEC

>P1;d2ogfa1
CHHHCHHHHHCCCCCCHHHHHHHHHHHHHHHHHHHHCCCEECCCCHHHHHHHHHHC-CCCCCEEEEEEECCCCCCCCEECCCC-CEEEEEEEECCEEEEEEEEEEHHHCEEEEEEEEE-
PSA

>P1;d2i52a1
----70957872-c37336004600950066018712736028931860267028204856104607040592a-b546064600203010307842030005049b77703361854c

>P1;d2ogfa1
47076a8246717a37466103500850185027722736016a338710660275-49421056060305b079a7670704-0204030408a10010103325966614424626-


Translating the sequences
----C***HHHC-CCCHHHHHHHHHHHHHHHHHHHHCCCEECCCCHHHHHHHHHHH*CCCCCEEEEEEEECCCC-CCEECCCC*EEEEEEEEECCEEEEEEEEEE***CEEEEEEEEE*
****CHHHHH*C*CCCHHHHHHHHHHHHHHHHHHHHCCCEECCCCHHHHHHHHHH*-CCCCCEEEEEEE*CCCC*CCEECCCC-*EEEEEEEECCEEEEEEEEEEHHHCEEEEEEEEE-

143560.tem
_________________________________
----CHHHHHHC-CCCHHHHHHHHHHHHHHHHHHHHCCCEECCCCHHHHHHHHHHH-CCCCCEEEEEEEECCCC-CCEECCCC-EEEEEEEEECCEEEEEEEEEEHHHCEEEEEEEEE-




Structural block scores
0	3	-	3.0	P	  75.0  4.5

5	10	H	3.7	M	  6.0  6.2

13	15	C	5.0	H	  7.5  6.8

16	35	H	5.0	H	  3.2  3.5

36	38	C	5.0	H	  4.0  4.0

39	40	E	5.0	H	  3.0  3.0

41	44	C	5.0	H	  5.5  5.1

45	55	H	4.8	H	  3.8  4.1

57	61	C	5.0	H	  4.8  4.0

62	69	E	4.8	H	  2.6  2.5

70	73	C	5.0	H	  6.6  5.9

75	76	C	5.0	H	  8.2  8.8

77	78	E	5.0	H	  5.0  6.5

79	82	C	5.0	H	  4.0  2.8

84	92	E	4.8	H	  1.0  1.4

93	94	C	5.0	H	  7.5  9.2

95	104	E	5.0	H	  1.8  1.1

105	107	H	3.0	P	  9.2  6.7

109	117	E	5.0	H	  4.1  3.9

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