Reading input alignment file to find conserved blocks of secondary structure

The input structure based alignment from Comparer
_____________________________________________

>P1;d2gjva1
CCHHHHHHHHHHHHHHHCCCEEEECCCCCCCCCCCCCCCEEEEEEEEEEEECCCCCCCCCEEEEEEEEEEEEEEC---CHHHHHHHHHHHHHHHCCCCCC-CCCCCCEEEEEEEEECHHHCEEEEEEEEEEEEEECCC

>P1;d3fz2a1
-CHHHHHHHHHHHHHHHCCCCEEEECCCC-----CCCCCCEEEEEEEEEEECC--------CCEEEEEEEEEEECCCCCHHHHHHC-CCCCCCCCCHHHHHHCC--EEEEEEEEEECCCCCEEEEEEEEEEEC-----
PSA

>P1;d2gjva1
09374005300640463178030432b5816615094a43000063350846929c5b45326040401000005---8685058005403800261804-70613063463651355692002002000004562a8

>P1;d3fz2a1
-249602510183069538605035522b-----08a1230000005c16635--------b44404000000044a066960581-83174198177178216--78827364362ab61000010330307-----


Translating the sequences
*CHHHHHHHHHHHHHHHCCCEEEE*CCCC*****CCCCCEEEEEEEEEEEECC********EEEEEEEEEEEEEC---CHHHHHHH*HHHHHHHCC****-*CC***EEEEEEEEECHHHCEEEEEEEEEEEE*****
-CHHHHHHHHHHHHHHHCCC*EEEECCCC-----CCCCC*EEEEEEEEEEECC--------**EEEEEEEEEEEC***CHHHHHH*-*******CCHHHH*HCC--EEEEEEEEEEC***CEEEEEEEEEEE*-----

143749.tem
_________________________________
-CHHHHHHHHHHHHHHHCCCEEEEECCCC-----CCCCCEEEEEEEEEEEECC--------EEEEEEEEEEEEEC---CHHHHHHH-HHHHHHHCCHHHH-HCC--EEEEEEEEEECHHHCEEEEEEEEEEEE-----




Structural block scores
2	16	H	5.0	H	  3.0  3.9

17	19	C	5.0	H	  5.3  5.7

20	24	E	4.2	M	  2.0  2.6

25	28	C	5.0	H	  6.6  5.1

29	33	-	3.0	P	  3.8  75.0

34	38	C	5.0	H	  5.5  4.3

39	50	E	4.8	H	  2.7  2.8

51	52	C	5.0	H	  7.5  4.0

53	60	-	3.0	P	  6.5  75.0

61	73	E	4.7	H	  1.3  2.1

75	77	-	3.0	P	  75.0  4.8

79	85	H	4.7	H	  4.6  5.0

87	93	H	3.0	P	  2.9  4.7

94	95	C	5.0	H	  4.0  4.5

96	99	H	3.0	P	  3.2  5.5

102	103	C	5.0	H	  3.0  3.5

104	105	-	3.0	P	  2.0  75.0

106	115	E	4.8	H	  3.7  5.4

117	119	H	3.0	P	  6.7  9.3

121	132	E	4.8	H	  0.7  1.4

133	137	-	3.0	P	  6.3  75.0

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