Reading input alignment file to find conserved blocks of secondary structure

The input structure based alignment from Comparer
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>P1;d1peqa1
--------------------------------------------------------CCCHHHHHHHHHCCCCCCCCCCHHHHHHHHHHHHHCHHHHCC--CCCCHHHHHHHHHHCCCCCHHHHCCCCHHHHHHHHHHH-HHCCCCCCCHHHHHHHHHHCCCCCCCCCCCCCCHHHHHHHHHHHHHCCC-----HHHHHHHHHHHHCCCCCCCHHHHHHCCCCCCCC

>P1;d2x1ya1
CCEEECCCCCEEECCHHHHHHHHHHHHCCCCCCCHHHHHHHHHCCCCCCEEHHHHHHHHHHHHHHCCC---C---CCCCHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHCCCCCCHHHHHCCHHHHHHHHHHCCHHHHHHC-CHHHHHHHHHHCCCCCCCCCCCCCCHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHCCCCCCCHHHHHHCCCCCC-C
PSA

>P1;d1peqa1
--------------------------------------------------------96716614733a676b66725882164007002253074511--92862670071027660036810660947103600950-373b291960770340035201316768500031100000000130715-----4a503610330049656075530310014859a

>P1;d2x1ya1
7241233878577056771572064019b098052750285029607640512401610070015236---a---a1420330001000200023009638035037003601838201820283054810760281051820160-229404602862012399586010100000000000420a4678401630451042003475916563031201446-a


Translating the sequences
--------------------------------------------------------***HHHHHHHHH***C***CCCHHHHHHHHHHHHH*HHHH*C--CCCCHHHHHHHHHHCCCCCHHHH**CCHHHHHHHHHHH-HH****C*CHHHHHHHHHHCCCCCCCCCCCCCCHHHHHHHHHHHHHCCC-----HHHHHHHHHHHHCCCCCCCHHHHHHCCCCCC*C
********************************************************HHHHHHHHH***---C---CCC*HHHHHHHHHHHHHHHHHHC**CCCCHHHHHHHHHHCCCCC*HHHHHCCHHHHHHHHHH**HHHHHHC-CHHHHHHHHHHCCCCCCCCCCCCCCHHHHHHHHHHHH*CCC*****HHHHHHHHHHHHCCCCCCCHHHHHHCCCCCC-C

48168.tem
_________________________________
--------------------------------------------------------HHHHHHHHHHHH---C---CCCHHHHHHHHHHHHHHHHHHHC--CCCCHHHHHHHHHHCCCCCHHHHHHCCHHHHHHHHHHH-HHHHHHC-CHHHHHHHHHHCCCCCCCCCCCCCCHHHHHHHHHHHHHCCC-----HHHHHHHHHHHHCCCCCCCHHHHHHCCCCCC-C




Structural block scores
0	55	-	3.0	P	  75.0  4.2

56	67	H	4.0	M	  5.3  2.6

68	70	-	3.0	P	  6.3  75.0

72	74	-	3.0	P	  6.3  75.0

75	77	C	5.0	H	  5.0  5.2

78	96	H	4.7	H	  3.0  0.8

98	99	-	3.0	P	  75.0  4.5

100	103	C	5.0	H	  6.2  4.0

104	113	H	5.0	H	  3.2  2.8

114	118	C	5.0	H	  3.0  2.8

119	124	H	4.0	M	  4.5  3.8

125	126	C	5.0	H	  4.5  2.5

127	137	H	4.8	H	  3.2  3.4

139	144	H	3.7	M	  5.9  3.0

148	157	H	5.0	H	  2.9  4.1

158	171	C	5.0	H	  3.0  3.4

172	184	H	4.8	H	  0.5  0.5

185	187	C	5.0	H	  4.3  4.8

188	192	-	3.0	P	  75.0  5.0

193	204	H	5.0	H	  3.0  2.2

205	211	C	5.0	H	  5.3  5.0

212	217	H	5.0	H	  2.8  3.0

218	223	C	5.0	H	  3.0  2.8

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