Reading input alignment file to find conserved blocks of secondary structure

The input structure based alignment from Comparer
_____________________________________________

>P1;d1ze3c2
-CCHHHCHHHCEEEECCCEEEEEECCCCCEEEEEEEECC-----EECC-CEEECCCEEEEEECCCCCCCCEEEEECCCCCCCCCCEECCCC-------

>P1;d2xg5a2
-C--CCCHHHCEEEEECCEEEEEECCCCCEEEEEEECCHHHHHHCCCC-CEEECCCEEEEECC---CCCCCEEEEECCCCCC-CEEEEEEECCEEEEC

>P1;d4ay0a2
-CCHHHCC-CCCCEEECCEEEE-CCCCCCEEEEEEEECC------CCC-CCEECCCCCEEEECCCCC-CEEEEEECCCCCCCCCCEEEECC-------

>P1;d4djma2
CCCHHHHHHHCEEEEECCEEEEECCCCCCCCCCCCEECC-----EECCCCCCCCCCCEEEEECCCC--------------------------------
PSA

>P1;d1ze3c2
-2559602640304269730101040346040250301a-----4706-616031754340803770699020203579763286380647-------

>P1;d2xg5a2
-b--841046010123bb003030405560201000256750477b1a-51505274555127---72b4020004276887-3013051bd660417

>P1;d4ay0a2
-3514630-6070637ca4030-0505350501504029------909-435012756430804bc1-67020304268785164365608-------

>P1;d4djma2
a9858623d7073672db40303030525071a8144ca-----75078454042653340212bd--------------------------------


Translating the sequences
-CCHHHCHHHCEEEE*CCEEEEE*CCCCCEEEEEEEECC-----**CC-C*EECCC*EEEEECCCCC*C**EEEE*CCCCCC*C*EE****-------
-C--**CHHHCEEEEECCEEEEE*CCCCCEEEEEEE*C********CC-C*EECCC*EEEE*C---C*C**EEEE*CCCCCC-C*EE***********
-CCHHHC*-*C**EEECCEEEE-*CCCCCEEEEEEEECC------*CC-C*EECCC**EEEECCCCC-C**EEEE*CCCCCC*C*EE****-------
*CCHHH*HHHCEEEEECCEEEEE*CCCCC******EECC-----**CC*C***CCC*EEEEECCCC--------------------------------

49584.tem
_________________________________
-CCHHHCHHHCEEEEECCEEEEE*CCCCCEEEEEEEECC-----**CC-C*EECCC*EEEEECCCCC*C**EEEE*CCCCCC*C*EE****-------




Structural block scores
1	2	C	4.7	H	  3.5  43.2  4.0  8.5

3	5	H	4.3	M	  6.7  29.0  3.7  6.3

7	9	H	4.3	M	  4.0  3.3  27.0  7.8

11	15	E	4.6	H	  3.0  1.4  4.6  5.0

16	17	C	5.0	H	  8.0  11.5  11.5  12.5

18	22	E	4.9	H	  1.0  1.2  16.4  2.0

24	28	C	5.0	H	  3.4  4.0  3.6  3.0

29	36	E	4.4	M	  1.8  0.6  1.9  4.4

37	38	C	4.7	H	  5.8  5.5  5.5  11.5

39	43	-	4.3	M	  75.0  4.6  75.0  75.0

44	45	*	1.6	P	  5.5  9.2  42.0  6.0

46	47	C	5.0	H	  3.0  5.8  4.5  3.5

51	52	E	4.3	M	  3.0  2.5  2.5  2.0

53	55	C	5.0	H	  3.7  4.7  3.3  4.0

57	61	E	4.7	H	  3.8  3.6  4.2  2.4

62	66	C	4.4	M	  3.4  47.8  5.8  20.6

69	70	*	2.3	P	  4.5  2.0  3.5  75.0

71	74	E	4.3	M	  1.0  0.5  1.2  75.0

76	81	C	4.3	M	  6.2  6.3  6.0  75.0

85	86	E	4.3	M	  5.5  2.0  4.5  75.0

87	90	*	2.3	P	  4.2  4.4  4.8  75.0

91	97	-	4.3	M	  75.0  5.4  75.0  75.0

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