Reading input alignment file to find conserved blocks of secondary structure

The input structure based alignment from Comparer
_____________________________________________

>P1;d1a79a1
----------------------CCHHHHHHHHHHHHH----CCCEEEECHHHCCCEEEECCCCCCCCC-CCCEEEEEEECCCCCCCHHHHHHHHHHHHC------CCEEEEEEECCCCCEEEECCCCCCC-

>P1;d1r0va1
-----------------------CHHHHHHHHHHHHH----CCCCCEEEC----CEEECC------------CEEEEEECCCCCCHHHHHHHCCC----------CCCCEEEEECCCCCEEEEECCCCCCC

>P1;d1r0va2
----------------------C-HHHHHHHHHHHHH----CCCEEEECHHHCCCEEEECCCCCHHHHHHCCEEEEECC-CCCCCHHHHHHHHHHHHHC------CCEEEEEEC-----CEEEEECCCCC-

>P1;d2gw6a1
CCCCCCCCHHHHHHHCCCCCCHHHHHHHHHHHHHHHHCCCCCCCEEEEECCCCEEEEECCCCC-----CCCCCEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCCCCEEEEEEECCCCCEEEEEEEC----
PSA

>P1;d1a79a1
----------------------a49814620463048----53210460992a00020067a153895-8021002014575b4987517801840873------816010020398470615656867a-

>P1;d1r0va1
-----------------------c8813450233037----6a4a0666d----51020a------------3010021376a37996137304b----------49402102045828062642565a8a

>P1;d1r0va2
----------------------b-8a24550442047----59240460992903020057175993367042003113-a6a3798517921640583------90500105b-----9616346569b-

>P1;d2gw6a1
907861854521603627208892040011014103874705406120049271000102287-----b44820000236b2a36a93062006003631868666020200204767616275182----


Translating the sequences
----------------------**HHHHHHHHHHHHH----CCCEEEE****C*CEEE*CCCC*****-*CC*EEEEEECCCCCC*HHHHHHHHHHHH*------CCEEEEEEECCCCCEEEE**CCCCC-
-----------------------*HHHHHHHHHHHHH----CCC**EE**----CEEE*C------------*EEEEEECCCCCCHHHHHHH***----------CC**EEEEECCCCCEEEEE*CCCCC*
----------------------*-HHHHHHHHHHHHH----CCCEEEE****C*CEEE*CCCC*******CC*EEEE**-CCCCCHHHHHHHHHHHHH*------CCEEEEEE*-----*EEEE*CCCCC-
************************HHHHHHHHHHHHH****CCCEEEE****C**EEE*CCCC-----**CC*EEEEEECCCCCCHHHHHHHHHHHHH*******CCEEEEEEECCCCCEEEEE**C----

53032.tem
_________________________________
----------------------**HHHHHHHHHHHHH----CCCEEEE****C*CEEE*CCCC*******CC*EEEEEECCCCCCHHHHHHHHHHHHH*------CCEEEEEEECCCCCEEEEE*CCCCC-




Structural block scores
0	21	-	4.3	M	  75.0  75.0  75.0  4.5

22	23	*	2.3	P	  7.2  43.8  43.2  5.5

24	36	H	5.0	H	  4.2  3.6  4.3  1.8

37	40	-	4.3	M	  75.0  75.0  75.0  4.5

41	43	C	5.0	H	  3.3  6.8  5.3  3.0

44	47	E	4.7	H	  2.8  5.6  3.5  2.2

48	51	*	1.6	P	  5.0  42.4  5.0  3.8

55	57	E	5.0	H	  0.7  1.0  0.7  0.3

59	62	C	4.5	M	  6.1  58.9  5.0  4.8

63	69	*	3.3	M	  16.1  75.0  6.0  55.8

70	71	C	4.3	M	  1.0  75.0  2.0  6.0

73	78	E	4.8	H	  1.2  0.7  1.3  0.8

79	84	C	4.9	H	  6.9  6.1  18.7  6.5

85	97	H	4.6	H	  4.9  21.4  5.0  3.5

99	104	-	4.3	M	  75.0  75.0  75.0  5.8

105	106	C	5.0	H	  4.5  6.5  4.5  3.0

107	113	E	4.7	H	  1.3  1.3  3.2  0.9

114	118	C	4.3	M	  6.2  5.4  75.0  6.0

119	123	E	4.7	H	  3.6  3.6  5.0  4.2

125	129	C	4.4	M	  7.5  6.9  7.5  47.0

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