Reading input alignment file to find conserved blocks of secondary structure

The input structure based alignment from Comparer
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>P1;d1cgme-
CCCCCCCCCCCCCCCCCCCCHHHHHHHHHCCCCCCCCCHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHCCCCCCCCCCCCC

>P1;d6saea-
CCCCCCHHHHHHHCCCEECHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCEEECCCCCHHHHHHHHHHHCCCCCHHHHHCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCEECHHHHHHHCCCCCC-------
PSA

>P1;d1cgme-
8363687a43517400400754038506925a45195591057228711670609166a7076870510300651086118614841454928337867848525764477973661365076317604640597a1514794266213286a39a8469

>P1;d6saea-
5072758906410550005286056107903a48056391035037505800731055763037965100141a603520770292072628928476b9a2889657716741370185036106602520777301142950185090827-------


Translating the sequences
CCCCCC*******CCC**C*HHHHHHHHH*CCCCCCC*HHHHHHHHHHHHCCCCCCCCCCCCCCCCC***CCCCC***HHHHHHHHCCCCC*****CCCCCCC*******HHHHHHHHHHHHHHHHHHHHHHHCCCC**CHHHHHHHCCCCCC*******
CCCCCCHHHHHHHCCCEECHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCEEECCCCCHHHHHHHHHHHCCCCCHHHHHCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCEECHHHHHHHCCCCCC-------

47195.tem
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CCCCCCHHHHHHHCCCEECHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCEEECCCCCHHHHHHHHHHHCCCCCHHHHHCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCEECHHHHHHHCCCCCC-------




Structural block scores
0	5	C	5.0	H	  5.7  4.3

6	12	H	3.0	P	  5.4  4.0

13	15	C	5.0	H	  1.3  3.3

16	17	E	3.0	P	  2.0  0.0

19	29	H	4.6	H	  4.5  4.0

30	36	C	5.0	H	  5.6  5.2

37	49	H	4.8	H	  4.2  3.8

50	66	C	5.0	H	  5.0  3.9

67	69	E	3.0	P	  1.3  0.3

70	74	C	5.0	H	  2.4  4.5

75	85	H	4.5	M	  4.3  3.4

86	90	C	5.0	H	  4.6  3.4

91	95	H	3.0	P	  4.6  6.2

96	102	C	5.0	H	  6.6  7.7

103	132	H	4.5	M	  4.6  4.1

133	136	C	5.0	H	  6.9  4.2

137	138	E	3.0	P	  3.0  1.0

140	146	H	5.0	H	  5.1  4.3

147	152	C	5.0	H	  5.1  4.3

153	159	-	3.0	P	  7.1  75.0

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