Reading input alignment file to find conserved blocks of secondary structure

The input structure based alignment from Comparer
_____________________________________________

>P1;d1vq8l1
CCHHHHCCCCCCCCCCCCCCCCCHHHHCCCCCCCCCCCCCCCCCCCCCC---------------------------------CCCCCHHHCCCEEEEEHHHHHHCCHHHCCCCCCCCEEEHHHCCCCCC--CCCEEEEECCCCCCCCCEEEECEECHHHHHHHHHCCCEEEECCCCCCCC----------

>P1;d1vq8o1
------------------------------------------------CCCCHHHHHHHHHHHHHHHHCCCHHHHHHHHHHC---CCHHH---CEEEEHHHHHHHCCC--------------------CCEEEEEEEEECCCCCCCCCEEEEEEECHHHHHHHHHH-CEEEEHHHHHHHCCCCCCEEECC
PSA

>P1;d1vq8l1
58998629b473491b766457a1c55558c8412586566b3a869aa---------------------------------a8957a9647811402056007407737a3767b340204710981a--90620204055707450201001039703740693b160421950685b----------

>P1;d1vq8o1
------------------------------------------------c2a688157007603710782b0a2047008304---56883---107050540266065--------------------b120000040407770836040002603b605730574-06013055119833606904305


Translating the sequences
************************************************C---------------------------------***CCHHH***EEEEEHHHHHH*CHH********************C--***EEEEECCCCCCCCCEEEE*EECHHHHHHHHH**CEEEE*******C----------
------------------------------------------------C*********************************---CCHHH---*EEEEHHHHHHHC**--------------------C**EEEEEEEECCCCCCCCCEEEEEEECHHHHHHHHHH-CEEEEHHHHHHHC**********

52080.tem
_________________________________
------------------------------------------------C------------------------------------CCHHH---EEEEEHHHHHHHCHH--------------------C--EEEEEEEECCCCCCCCCEEEEEEECHHHHHHHHHH-CEEEEHHHHHHHC----------




Structural block scores
0	47	-	3.0	P	  6.6  75.0

49	84	-	3.0	P	  69.5  10.1

85	86	C	5.0	H	  6.0  5.5

87	89	H	5.0	H	  8.5  6.3

90	92	-	3.0	P	  6.3  75.0

93	97	E	4.6	H	  1.6  2.6

98	104	H	4.7	H	  3.1  3.3

106	107	H	3.0	P	  7.0  5.5

108	127	-	3.0	P	  4.7  75.0

129	130	-	3.0	P	  75.0  1.5

131	138	E	4.2	M	  2.9  1.0

139	147	C	5.0	H	  3.7  4.2

148	154	E	4.7	H	  0.6  1.7

156	165	H	4.8	H	  4.8  4.8

168	171	E	5.0	H	  3.0  2.5

172	178	H	3.0	P	  4.9  4.1

180	189	-	3.0	P	  75.0  3.6

>>>>>>