Reading input alignment file to find conserved blocks of secondary structure

The input structure based alignment from Comparer
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>P1;d2vy8a-
CCCCHHHHHHHHHHHHHHHCHH----HHHHHHHH-CHHHHHCCHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCCCCCCEEEECCCEEEECCCCCCCEEEECCCCEEEECCEEEEECCCCCCCCCCCCCC

>P1;d5d9ac2
---CHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHCCCHHHHHCHHHHHHHHHCCCCCHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHCC--------CCCCCC-CCCCCCCCCCCCCEECCCCCCEECCCCEECCCCCCC-CCCC----
PSA

>P1;d2vy8a-
43a6962130040013007408----70162048-62660073830750170028943030001014207822787726122000000000093663a68291020613460419a51800626844350401935032058ba5355a949f

>P1;d5d9ac2
---8b625402720320056009989202202755547400706105600520377514700760374036236697131111100000034b--------840304-9350133762800223787230401a8513485129-0562----


Translating the sequences
***CHHHHHHHHHHHHHHH*HH----HHHHHHHH-CHHHHH*CHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHH*CC********CEEEEC*CEEEECCCCCCCEEEECCCCEEEECCEEEEECCCCC*CCCC****
---CHHHHHHHHHHHHHHHH*******HHHHHHH*C*HHHHHCHHHHHHHHHCCCCCHHHHHHHHHHHHHH*****CCCHHHHHHHHHHHHCC--------C****C-C****CCCCCCC*EE*CCCC*EE*CC*EE**CCCCC-CCCC----

418740.tem
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---CHHHHHHHHHHHHHHHHHH----HHHHHHHH-CHHHHHHCHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHCC--------CEEEEC-CEEEECCCCCCCEEEECCCCEEEECCEEEEECCCCC-CCCC----




Structural block scores
0	2	-	3.0	P	  5.8  75.0

4	21	H	4.7	H	  2.7  3.1

22	25	-	3.0	P	  75.0  8.8

26	33	H	4.8	H	  3.5  2.5

36	41	H	4.3	M	  3.5  3.7

43	51	H	5.0	H	  3.4  2.8

52	56	C	5.0	H	  4.6  4.4

57	75	H	4.5	M	  2.9  3.9

76	78	C	5.0	H	  5.0  3.7

79	90	H	4.8	H	  0.4  0.7

91	92	C	5.0	H	  4.5  7.8

93	100	-	3.0	P	  5.6  75.0

102	105	E	3.0	P	  0.8  1.8

109	112	E	3.0	P	  3.5  2.2

113	119	C	5.0	H	  4.9  4.1

120	123	E	4.0	M	  3.5  1.8

124	127	C	5.0	H	  4.8  6.0

128	131	E	4.0	M	  2.2  1.8

132	133	C	5.0	H	  5.0  5.8

134	138	E	3.8	M	  2.6  4.2

139	143	C	5.0	H	  7.0  5.0

145	148	C	5.0	H	  5.9  3.2

149	152	-	3.0	P	  11.1  75.0

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