Reading input alignment file to find conserved blocks of secondary structure

The input structure based alignment from Comparer
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>P1;d2cwya1
-----------------CCCHHHHHHHHHCCCHHHHHHHHHHHHHHCC--HHHHHHHHHHHHHHHHHHHHHC-CC--CCHHHHHHHHHHHCCCCCCC-CCCHHHHHHHHHHHHCC------------------------------

>P1;d2ijqa1
CCCCCEECCCEECCHHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHCCCCCCHHHCCHHHHHHHHHHHHHCHHHHCCCCCCCCCCCCCCCHHHHHHHHHCC
PSA

>P1;d2cwya1
-----------------9071880252067160730374055425919--b563400300010020023465-a6--80582063036308a05162-b06056005404750a3------------------------------

>P1;d2ijqa1
d724234b655153750150021002000344163023003301761a9a53202001000100200241346843930382066017406b0456001040640261067018625305c130405874152396038207719


Translating the sequences
-----------------***HHHHHHHHHCCCHHHHHHHHHHHHHHCC--HHHHHHHHHHHHHHHHHHHHH*-CC--**HHHHHHHHHHHCCCCCC*-*CCHHHHHHHHHHHH*C------------------------------
*****************HHHHHHHHHHHHCCCHHHHHHHHHHH***CC***HHHHHHHHHHHHHHHHHHHHH*CC**HHHHHHHHHHHHHCCCCCCH*HCCHHHHHHHHHHHHHC******************************

140663.tem
_________________________________
-----------------HHHHHHHHHHHHCCCHHHHHHHHHHHHHHCC--HHHHHHHHHHHHHHHHHHHHHH-CC--HHHHHHHHHHHHHCCCCCCH-HCCHHHHHHHHHHHHHC------------------------------




Structural block scores
0	16	-	3.0	P	  75.0  4.9

17	28	H	4.5	M	  4.0  0.9

29	31	C	5.0	H	  4.7  3.7

32	45	H	4.6	H	  3.9  2.5

46	47	C	5.0	H	  5.0  5.8

48	49	-	3.0	P	  75.0  9.8

50	71	H	4.8	H	  2.5  1.4

73	74	C	5.0	H	  8.2  6.0

75	76	-	3.0	P	  75.0  6.0

77	89	H	4.7	H	  3.4  3.1

90	95	C	5.0	H	  5.1  5.4

99	100	C	5.0	H	  3.0  2.0

101	113	H	4.8	H	  3.6  3.2

115	144	-	3.0	P	  75.0  4.1

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