Reading input alignment file to find conserved blocks of secondary structure

The input structure based alignment from Comparer
_____________________________________________

>P1;d2dm9a1
CHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHCCCEEEEECCHHHHHHHHHCHHHHHHHCC------CC-EEEEC-CCCC---CCCEEEEEECCCCCEEEEEHHHHHHHCHHHHHHHHHHHHHC--

>P1;d3k5ba1
CHHHHHHHHHHHCCCCCC-CCCCCCCCCC------------CCCCCC--CCCCCCC-----------------------------CCCCCCCCCCC-CCCCCCCCCCCCCCCCCC--CCHHHHCC------

>P1;d4efae2
CHHHHHHHHHHHHHCC--HHHHHHHHHHHHHHHHHHHCCCEEEEEECCCCHHHHCCCHHHHHHHHHHHCCCCCCCEEEECCCCCCCCCCCCEEEEECCCCCCEEEEEHHHHHHHHHHHHHHHHHHHHCCCC
PSA

>P1;d2dm9a1
732653156366718917585106300710160068093660200029700900572384048517------80-70731-853b---0200010105736552400141216553983577467868f--

>P1;d3k5ba1
b64844557756765439-9735774299------------a6a226--736584e-----------------------------85665344423-ab8b69667688882782--8449936e------

>P1;d4efae2
b738644872594076--6a60455026100400260535503020074018005603750373057619a380660502b8315898120000010757865240012241656267354736575867b


Translating the sequences
CHHHHHHHHHHHHH**CCHHHHHHHHHHHHHHHHHHHCCCEEEEECC***HHHH**CHHHHHHH**------CC-EEEEC-CCCC---CCCEEEEE*CCCCCEEEEEHHHHHHHCHHHHHHHHHHHH*C--
CHHHHHHHHHHH**CCCC-**********------------****CC--C****CC-----------------------------CCCCCC*****-CCCCC************C--**HHHH**------
CHHHHHHHHHHHHHCC--HHHHHHHHHHHHHHHHHHHCCCEEEEE*C**CHHHHCCCHHHHHHH********CC*EEEEC*CCCCCCCCCCEEEEE*CCCCCEEEEEHHHHHHH*HHHHHHHHHHHH*C**

160527.tem
_________________________________
CHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHCCCEEEEECC**CHHHHCCCHHHHHHH**------CC-EEEEC-CCCCCCCCCCEEEEE*CCCCCEEEEEHHHHHHHCHHHHHHHHHHHH*C--




Structural block scores
1	13	H	4.8	H	  4.2  5.7  5.2

14	17	C	4.0	M	  6.2  5.2  40.8

18	36	H	4.0	M	  3.0  38.8  3.0

37	39	C	4.0	M	  6.0  75.0  4.3

40	44	E	4.0	M	  1.6  20.8  2.0

45	46	C	4.5	M	  1.0  4.0  0.0

47	48	*	2.7	P	  8.0  75.0  5.5

50	53	H	4.0	M	  2.2  5.5  2.2

54	56	C	4.0	M	  4.7  31.2  3.7

57	63	H	4.0	M	  4.6  75.0  4.0

64	65	*	2.7	P	  4.0  75.0  2.5

66	71	-	4.0	M	  75.0  75.0  6.1

72	73	C	4.0	M	  4.0  75.0  4.0

75	78	E	4.0	M	  4.2  75.0  2.8

81	90	C	4.3	M	  25.4  33.3  4.5

91	95	E	4.0	M	  0.4  3.4  0.2

97	101	C	5.0	H	  5.2  9.5  6.6

102	106	E	4.0	M	  2.2  6.8  2.2

107	113	H	4.0	M	  2.9  7.0  3.0

115	126	H	4.3	M	  6.1  29.8  5.0

129	130	-	4.0	M	  75.0  75.0  9.2

>>>>>>