Reading input alignment file to find conserved blocks of secondary structure

The input structure based alignment from Comparer
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>P1;d2azea1
CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-----HHHHCCCCCCCHHHCC----CCCCEEEEECCCCCEEEEECCCCC----CEEEEECCCEEEEEHHHHHHHCCCCCCHHHCCCCHHHHHHHHHCCCHHHHHHHHHHHHCCCCCCC

>P1;d2azeb1
-CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCHHHHHHCCCCHHHHHCCCCCCCCCCCEEECCCCCEEEEEECC--CCEEEEEECCCCCCEEECCCCC---------------------------------------------------------

>P1;d5tuvb-
-CCCCCC---CCCCCCCCHHHHHHHHHHHCCC-CCCCCHHHHHCCCCCC-CHHHHC---CCCEEEEECCCCCCCCCCCCCCCCCCCCCC-CCCCCCEEEEE--C---------------------------------------------------------
PSA

>P1;d2azea1
a898768574667636446761774347002300551164557-----76466a897378b647----9282543616a907363634c668----84646177946524023301637100402717059842950471059933710440168718d38

>P1;d2azeb1
-9988777868777567767767768675577666675a73575676648522973404975143271299095764839--9786572708859163660648---------------------------------------------------------

>P1;d5tuvb-
-7b8688---9868779888767776776566-877a5a8577666775-634976---da72542813bb0957527578b5475561-08549383560--a---------------------------------------------------------


Translating the sequences
**HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH*HHHHH-----HHHH*CCCCCC***CC----CCCCEEEEECCCCC**EEECC*CC----*EEEE*CC*********************************************************
-CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCHHHHH*CCCCHHHHHCCCCCCCCCCCEEECCCCCEEEEE*CC--CCEEE***CCCCCCEEE***CC---------------------------------------------------------
-C*****---********HHHHHHHHHHH***-****CHHHHH*CCCC*-*HH**C---CCC**EEECCCCC*****CCCCCCC***CC-CCCCCCEEEEE--C---------------------------------------------------------

144074.tem
_________________________________
-CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCHHHHH*CCCCHHHHHCCCCCCCCCCCEEECCCCCEEEEECCCCCCCEEECC*CCCCCCEEEEE*CC---------------------------------------------------------




Structural block scores
2	36	H	4.3	M	  4.7  6.7  15.1

38	42	H	5.0	H	  5.4  6.5  7.5

44	47	C	4.0	M	  75.0  6.2  6.5

48	52	H	4.2	M	  5.8  4.2  18.6

53	63	C	4.1	M	  7.4  4.8  25.9

64	66	E	4.0	M	  75.0  4.0  4.7

67	71	C	4.8	H	  19.2  4.2  5.4

72	76	E	4.0	M	  3.8  6.2  5.6

77	83	C	4.3	M	  5.9  26.6  6.8

84	86	E	4.0	M	  4.0  6.3  5.7

87	88	C	4.0	M	  8.2  4.5  3.5

90	95	C	4.3	M	  52.3  5.2  4.8

96	100	E	4.4	M	  5.6  4.2  4.4

102	103	C	4.5	M	  7.0  6.0  42.8

104	160	-	4.0	M	  4.1  75.0  75.0

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