Reading input alignment file to find conserved blocks of secondary structure

The input structure based alignment from Comparer
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>P1;d1wn2a-
CCCEEEEEEEECCCCCCHHHHHHHHHHHHHHHHHHHHHHCHHHHHHHHHC--------------CCCEEEEEECCHHHHHHHHHHHHHCCCCEEEEECCCCC----CCC-------CCCEEEEEEEEEEHHHHHHHHCCCEEC-

>P1;d2gaxa1
-CCEEEECCCCCC--CCHHHHHHHHHHC-CHHHHHC--------HHHCCCCEECCCCCEECCCCCCCEECCC--CHHHHHHHHHHHHHCCCCCCCEECCCCCCCHHHHHHHHCCCCCCCCCEEECEEEEHHHHHHHCCCCCCCC
PSA

>P1;d1wn2a-
b6711000000231a08ab4175016401750174036745a21410575--------------b453330307438405812640582a00101072ba08----507-------9511000000000273046005b1974-

>P1;d2gaxa1
-481200000168--0587218404770-8704841--------7903393654d7a756a36150744301--837101401420584a181212043184a8884477357626376050000021659406601881873a


Translating the sequences
*CCEEEEEEEECC**CCHHHHHHHHHHH*HHHHHHH********HHHHHC--------------CCCEEEEE**CHHHHHHHHHHHHHCCCCEEEEECCCCC----***-------CCCEEEEEEEEEEHHHHHHHHCCCEEC-
-CCEEEE****CC--CCHHHHHHHHHH*-*HHHHH*--------HHH**C**************CCCEE***--CHHHHHHHHHHHHHCCCC***EECCCCC****HHH*******CCC**EEE*EEEEHHHHHHH*CCC**C*

102462.tem
_________________________________
-CCEEEEEEEECC--CCHHHHHHHHHHH-HHHHHHH--------HHHHHC--------------CCCEEEEE--CHHHHHHHHHHHHHCCCCEEEEECCCCC----HHH-------CCCEEEEEEEEEEHHHHHHHHCCCEEC-




Structural block scores
1	2	C	5.0	H	  6.5  6.0

3	10	E	4.0	M	  0.2  0.5

11	12	C	5.0	H	  2.5  7.0

13	14	-	3.0	P	  5.8  75.0

15	16	C	5.0	H	  4.0  2.5

17	27	H	4.8	H	  4.5  4.4

29	35	H	4.4	M	  3.4  4.6

36	43	-	3.0	P	  4.8  75.0

44	48	H	4.2	M	  3.4  4.4

50	63	-	3.0	P	  75.0  6.2

64	66	C	5.0	H	  6.8  4.0

67	71	E	3.8	M	  2.4  2.4

72	73	-	3.0	P	  3.5  75.0

75	87	H	5.0	H	  4.2  2.8

88	91	C	5.0	H	  3.1  5.9

92	96	E	3.8	M	  1.8  1.2

97	101	C	5.0	H	  6.4  4.0

102	105	-	3.0	P	  75.0  8.6

106	108	H	3.0	P	  4.0  5.0

109	115	-	3.0	P	  75.0  5.1

116	118	C	5.0	H	  5.0  5.3

119	128	E	4.4	M	  0.1  1.4

129	136	H	4.8	H	  2.8  3.9

137	139	C	5.0	H	  5.8  5.7

140	141	E	3.0	P	  8.0  7.5

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