Reading input alignment file to find conserved blocks of secondary structure

The input structure based alignment from Comparer
_____________________________________________

>P1;d3hola3
CCCCCCCCCCCCCCCCCCCCCCCCEEEEECCCCCCCCCCCCCCCCEEECCCCCCCCCCHHHHC----------------CCC--CEEECCCCCCCCCEEEEEEEECCCCCC----CCCEEEEEEECCCC

>P1;d3hola4
----------------------CEEEEEECCC---------CEEEECCCCCCCCEEEEC---CEEEECCCCCCEEEEEEEECCEEEEEEEECCCCCCEEEEEEEECC----CCCCCEEEEEEEEEC-CC
PSA

>P1;d3hola3
8898baa8a9aa97a49a7767230301532537a887847679356086160750137a408----------------907--64415936a9486616240203728ba----9330060602477b

>P1;d3hola4
----------------------4402343268---------776790907460310007---95507095b76325153708a621002010583883143501227----a76946650405023-7c


Translating the sequences
**********************C*EEEEECCC*********C***EEECCCCCC****H***C----------------**C--*EEE***CCCCCCEEEEEEEECC****----C**EEEEEEEC*CC
----------------------CEEEEEECCC---------CEEEE**CCCCCCEEEE*---C****************EEC**EEEEEEECCCCCCEEEEEEEECC----****CEEEEEEEEEC-CC

310592.tem
_________________________________
----------------------CEEEEEECCC---------CEEEEEECCCCCCEEEEH---C----------------EEC--EEEEEEECCCCCCEEEEEEEECC--------CEEEEEEEEEC-CC




Structural block scores
0	21	-	3.0	P	  8.7  75.0

23	28	E	4.7	H	  2.0  2.7

29	31	C	5.0	H	  3.3  5.3

32	40	-	3.0	P	  6.9  75.0

42	47	E	3.3	M	  5.0  6.3

48	53	C	5.0	H	  4.7  3.3

54	57	E	3.0	P	  2.2  0.2

59	61	-	3.0	P	  4.8  75.0

63	78	-	3.0	P	  75.0  4.7

79	80	E	3.0	P	  4.5  3.5

82	83	-	3.0	P	  75.0  8.2

84	90	E	3.9	M	  4.6  0.9

91	96	C	5.0	H	  7.2  5.3

97	104	E	5.0	H	  2.6  2.4

105	106	C	5.0	H	  5.0  4.5

107	114	-	3.0	P	  41.5  41.6

116	124	E	4.6	H	  2.2  3.1

127	128	C	5.0	H	  9.2  9.8

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