Reading input alignment file to find conserved blocks of secondary structure

The input structure based alignment from Comparer
_____________________________________________

>P1;d1svdm1
CCCCCCC--CCCCCCCCCCCCCCHHHHHHHHHHHHHCCCEEEEEEECHHHCCCC-------------CCEEECCCCCCCCCHHHHHHHHHHHHHHCCCCEEEEEEEEC--CCCEEEEEEEEECC-----------------------------------

>P1;d1wdds-
--CCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHCCCEEEEEEEC--CCCCCCCCCCCCCCCCCCCCEEECCCCCCCCCHHHHHHHHHHHHHHCCCCEEEEEEEEC--CCCEEEEEEEEECCCCC--------------------------------

>P1;d4f0hb-
--------CCCCCCCCCCCCCCCHHHHHHHHHHHHHCCCEEEEEEECCCCCCCC-------------CCEECCCCCCCCCCHHHHHHHHHHHHHHCCCCEEEEEEEECCCCCCEEEEEEEEECCCCCCCEEEEEEECCCCCEEEEEEEHHHHCCHHHCC
PSA

>P1;d1svdm1
caa8789--7932a63075760848304720850074a1100010045842a59-------------a064168117b287285006106505844691001000428--95873213000320-----------------------------------

>P1;d1wdds-
--ba7599c4721a722668917863136304501739110001125--704552776759944135a074168126c196076017106402844560002000229--969541130102408b5--------------------------------

>P1;d4f0hb-
--------5403415309697074860473055027490101011004024826-------------a0652b9136a18617602830330175275200100040a8ab4673313000310a8020144456839a96275744041054679611


Translating the sequences
**CCCCC--CCCCCCCCCCCCCCHHHHHHHHHHHHHCCCEEEEEEEC***CCCC-------------CCEEECCCCCCCCCHHHHHHHHHHHHHHCCCCEEEEEEEEC--CCCEEEEEEEEECC-----------------------------------
--CCCCC*CCCCCCCCCCCCCCCHHHHHHHHHHHHHCCCEEEEEEEC--CCCCC*************CCEEECCCCCCCCCHHHHHHHHHHHHHHCCCCEEEEEEEEC--CCCEEEEEEEEECCCCC--------------------------------
--------CCCCCCCCCCCCCCCHHHHHHHHHHHHHCCCEEEEEEEC**CCCCC-------------CCEE*CCCCCCCCCHHHHHHHHHHHHHHCCCCEEEEEEEEC**CCCEEEEEEEEECCCCC********************************

55239.tem
_________________________________
--CCCCC-CCCCCCCCCCCCCCCHHHHHHHHHHHHHCCCEEEEEEEC**CCCCC-------------CCEEECCCCCCCCCHHHHHHHHHHHHHHCCCCEEEEEEEEC--CCCEEEEEEEEECCCCC--------------------------------




Structural block scores
0	1	-	4.0	M	  11.5  75.0  75.0

2	6	C	4.0	M	  8.5  8.6  75.0

8	22	C	4.9	H	  9.9  5.7  4.2

23	35	H	5.0	H	  3.7  3.6  3.9

36	38	C	5.0	H	  5.2  4.3  4.3

39	45	E	5.0	H	  0.3  0.7  0.6

47	48	*	2.7	P	  6.5  75.0  2.0

49	53	C	4.8	H	  6.1  4.2  4.4

54	66	-	4.0	M	  75.0  5.3  75.0

67	68	C	5.0	H	  5.2  5.2  5.2

69	71	E	4.7	H	  3.7  4.0  4.3

72	80	C	5.0	H	  5.7  5.7  6.2

81	94	H	5.0	H	  3.6  3.3  3.3

95	98	C	5.0	H	  5.0  3.8  4.0

99	106	E	5.0	H	  0.9  0.8  0.6

108	109	-	4.0	M	  75.0  75.0  9.2

110	112	C	5.0	H	  7.3  8.0  7.2

113	121	E	5.0	H	  2.1  1.9  2.2

122	126	C	4.4	M	  45.4  5.7  3.9

127	158	-	4.0	M	  75.0  75.0  4.5

>>>>>>