Reading input alignment file to find conserved blocks of secondary structure

The input structure based alignment from Comparer
_____________________________________________

>P1;d3e9ta1
--CEEEECCCEEEEECCCCEEEEEEEEEC-CCCCCEEEEEEEECCCCCCCCCCCCCEEEEEECCCCCEEEEEEECCCCCCCCCCEEEEEEEECCCC-------------------------------CCEECCCCEEEEEEECC--------------

>P1;d3e9ua1
--CEEEECCCEEECCCCCCCCCEEEEEEC-CCCCCEEEEEEEECCCCCC-CCCCCCEEEEEECCCCCEEEECCCCCCCCCCCCEEEEEEEECCCEECCCCCCHHHHHHHCCCCHHHCCHHHHHHHHHCCEECCCCEEEEEEECCCCCHHHHHHHHHCC

>P1;d3fsoa1
-CCEEEECCCEEEEEHHHCEEEEEEEEECCC-CCCEEEEEEEEECCCCCCCCCCCCEEEEEECCCCCEEEEEEECCCC----CEEEEEEEEEEEEC-------------------------------CCEECCCCEEEEEEECC--------------

>P1;d3gina-
CEEEEEECCCEEEEECCCCEEEEEEEEECCCCCCCEEEEEEEEECCCCCCCCCCCCEEEEEECCCCCEEEEEEECCCCCCCCCCEEEEEEEEEEECC------------------------------EEEECCCCEEEEEEECCCC------------
PSA

>P1;d3e9ta1
--1402045141415062a413020004a-647750103030453804397104356550404574433405050354b8939633030301724b-------------------------------b0811934503030314--------------

>P1;d3e9ua1
--530005558251303395240302058-a275301021505457054-600601574050669454340405045462881512020103905117a4b6166076047368861588057328720524a432050403027743572678787a

>P1;d3fsoa1
-603000566515140358105020305635-88402020506449061a4004347350506494572305060353----44230303068344-------------------------------b0622924401000456--------------

>P1;d3gina-
a30401056451616063a403020007806484304031606448063a61074357413075844635050104549753942502030670614------------------------------8053394230402040318------------


Translating the sequences
--CEEEECCCEEEEECCCCEEEEEEEEEC-CCCCCEEEEEEEE*CCCCCCCCCCCCEEEEEECCCCCEEEEEEECCCCCCCCC*EEEEEEEE***C-------------------------------CCEECCCCEEEEEEECC--------------
--CEEEECCCEEE**CCCC***EEEEEEC-CCCCCEEEEEEEE*CCCCC-CCCCCCEEEEEECCCCCEEEE***CCCCCCCCC*EEEEEEE***E********************************CCEECCCCEEEEEEECC**************
-*CEEEECCCEEEEE***CEEEEEEEEEC*C-CCCEEEEEEEE*CCCCCCCCCCCCEEEEEECCCCCEEEEEEECCCC----C*EEEEEEEE**EC-------------------------------CCEECCCCEEEEEEECC--------------
***EEEECCCEEEEECCCCEEEEEEEEEC*CCCCCEEEEEEEE*CCCCCCCCCCCCEEEEEECCCCCEEEEEEECCCCCCCCC*EEEEEEEE**EC*------------------------------**EECCCCEEEEEEECC**------------

141072.tem
_________________________________
-*CEEEECCCEEEEECCCCEEEEEEEEEC*CCCCCEEEEEEEE*CCCCCCCCCCCCEEEEEECCCCCEEEEEEECCCCCCCCC*EEEEEEEE**EC*------------------------------CCEECCCCEEEEEEECC**------------




Structural block scores
3	6	E	5.0	H	  1.5  0.8  0.8  1.2

7	9	C	5.0	H	  3.3  5.0  5.7  5.0

10	14	E	4.7	H	  3.0  3.8  3.2  3.8

15	18	C	4.5	M	  4.6  3.8  4.0  4.9

19	27	E	4.8	H	  1.6  2.3  1.8  1.8

30	34	C	4.9	H	  5.8  5.5  20.0  5.0

35	42	E	5.0	H	  1.4  1.8  1.9  2.5

44	55	C	4.9	H	  3.9  9.1  3.8  4.4

56	61	E	5.0	H	  3.3  3.5  3.3  3.3

62	66	C	5.0	H	  4.8  6.0  5.6  5.6

67	73	E	4.7	H	  2.9  2.9  3.3  2.9

74	82	C	4.7	H	  5.8  4.2  35.0  5.1

84	91	E	4.9	H	  1.6  1.1  2.1  2.2

92	93	*	1.0	P	  4.5  4.5  5.5  3.5

97	126	-	4.3	M	  75.0  5.4  75.0  75.0

127	128	C	4.3	M	  5.8  1.0  5.8  4.0

129	130	E	5.0	H	  4.5  3.5  4.0  4.0

131	134	C	5.0	H	  4.2  5.4  4.2  4.5

135	141	E	5.0	H	  2.0  2.0  1.3  1.9

142	143	C	5.0	H	  2.5  1.0  5.5  1.5

144	145	*	3.5	M	  75.0  7.0  75.0  4.5

146	157	-	4.3	M	  75.0  6.2  75.0  75.0

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