Reading input alignment file to find conserved blocks of secondary structure

The input structure based alignment from Comparer
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>P1;d1gpqa-
-CCCCHHHHHHCCCCHHHHHHHHCCC-CCCCHHHH-CCEECCCEEEEECCEEEEEEEEECCCCCCCEEEEEEECCCCCCEEEEEEEEEHHHC-------EEEEEEECCCHHHCCHHHHHHHHHHHCHHHHCCCCCCC

>P1;d4ps6a1
CEECCHHHHCCCHHHHHHHHC-CCCCCCCCHHHHHCCCCCCCEEEEEECCEEEEEEEEECCCCCCCEEEEEEEECCCCCEEEEEEECCCCCCCCCCHHHCCEEEEECCC---CHHHHHHC-CCHHHCC------CCC
PSA

>P1;d1gpqa-
-b7310150066a91580067028a3-913a0058-306458025040c935030011043a55b422000010775550000004259969-------7282420404a804950350040004540387597146

>P1;d4ps6a1
872440450084980681197-19b39a13810450615073042362aa75100020044a558312000004284630100104048849508303730833307a0---76604600-7206738------a08


Translating the sequences
-**CCHHHHHHC***HHHHHH*HCCC-CCC*HHHH-CCEECC*EEEEECCEEEEEEEEECCCCCCCEEEEEEE*CCCCCEEEEEEEEEHHHC-------EEEEEEECCC***C*HHHHHH*HHHH*HH******CCC
*EECCHHHH**CHHHHHHHH*-*CCC*CCCHHHHH*CC**CCEEEEEECCEEEEEEEEECCCCCCCEEEEEEEECCCCCEEEEEEE*****C*********EEEEECCC---CHHHHHH*-**HHH**------CCC

89872.tem
_________________________________
-EECCHHHHHHCHHHHHHHHH-HCCC-CCCHHHHH-CCEECCEEEEEECCEEEEEEEEECCCCCCCEEEEEEEECCCCCEEEEEEEEEHHHC-------EEEEEEECCC---CHHHHHHH-HHHHHHH------CCC




Structural block scores
1	2	E	3.0	P	  9.2  4.5

3	4	C	5.0	H	  2.0  4.0

5	10	H	4.3	M	  2.0  2.8

12	20	H	4.1	M	  5.2  5.4

23	25	C	5.0	H	  7.2  7.8

27	29	C	5.0	H	  4.3  4.8

30	34	H	4.6	H	  4.7  3.6

36	37	C	5.0	H	  1.5  3.5

38	39	E	3.0	P	  5.0  2.5

40	41	C	5.0	H	  6.5  5.0

42	47	E	4.7	H	  1.8  2.8

48	49	C	5.0	H	  10.8  10.5

50	58	E	5.0	H	  1.4  1.7

59	65	C	5.0	H	  6.1  5.6

66	73	E	4.8	H	  0.6  0.9

74	78	C	5.0	H	  5.8  4.6

79	87	E	4.6	H	  1.2  1.1

88	90	H	3.0	P	  8.0  6.7

92	98	-	3.0	P	  75.0  3.7

99	105	E	4.4	M	  3.6  2.9

106	108	C	5.0	H	  2.7  5.8

109	111	-	3.0	P	  6.2  75.0

113	119	H	4.4	M	  3.1  3.1

121	127	H	3.6	M	  1.9  4.7

128	133	-	3.0	P	  6.5  75.0

134	136	C	5.0	H	  3.7  6.2

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