Reading input alignment file to find conserved blocks of secondary structure

The input structure based alignment from Comparer
_____________________________________________

>P1;d1a79a2
--------CEEEEEECCEEEECCHHHHHHHHHCCCCEECCCCEEEEHHHHHHHHHCCCEEEECCCCCCCCHHHHHHHHHHHC-

>P1;d1r0va3
CCCCCCCCCEEEEEECCEEEEC---CCHHHHCCCCCEEECCEEEECHHHHHHHHHCCCEEEC-----CCCHHHHHHHHHHHCC

>P1;d1r11a3
--------------CCCCEEEECC---HHHHCCCCCEECCCEEEECHHHHHHHHHCCCCCCC-------CHHHHHHHHHCCC-
PSA

>P1;d1a79a2
--------51404078740106697017503559207357a30104093015015363030238898326485046216835-

>P1;d1r0va3
da692a0360405067550308---42603552611737b9402050820260144a30706-----518594017227636a

>P1;d1r11a3
--------------b885241814---860466a20848a9503040720250055952828-------8597047118925-


Translating the sequences
--------CEEEEEECCEEEECC****HHHH*CCCCEECCC*EEE*HHHHHHHHHCCCEEE******CCCHHHHHHHHHHHC-
********CEEEEEECCEEEEC---**HHHHCCCCCEE*CCEEEECHHHHHHHHHCCCEEEC-----CCCHHHHHHHHHHHC*
--------------*CC*EEE*C*---HHHHCCCCCEECCCEEEECHHHHHHHHHCCC***C-------CHHHHHHHHH**C-

55267.tem
_________________________________
--------CEEEEEECCEEEECC*-**HHHHCCCCCEECCCEEEECHHHHHHHHHCCCEEEC-----CCCHHHHHHHHHHHC-




Structural block scores
0	7	-	4.0	M	  75.0  6.8  75.0

9	14	E	4.0	M	  2.7  2.5  64.4

15	16	C	5.0	H	  7.5  6.0  8.0

17	20	E	4.8	H	  1.2  2.0  3.0

21	22	C	4.0	M	  6.0  41.5  4.5

25	26	*	2.7	P	  0.5  3.0  75.0

27	30	H	5.0	H	  3.8  3.5  4.5

31	35	C	4.8	H	  4.2  3.0  4.9

36	37	E	5.0	H	  5.0  5.0  6.0

38	40	C	4.7	H	  7.5  9.2  9.2

41	44	E	4.8	H	  1.0  1.5  2.0

46	54	H	5.0	H	  2.7  2.6  2.3

55	57	C	5.0	H	  4.0  5.8  6.3

58	60	E	4.0	M	  1.0  2.3  4.0

62	66	-	4.0	M	  7.2  75.0  75.0

67	69	C	4.3	M	  3.7  4.7  52.7

70	80	H	4.8	H	  4.3  4.2  4.8

>>>>>>