Reading input alignment file to find conserved blocks of secondary structure

The input structure based alignment from Comparer
_____________________________________________

>P1;d3luua-
CCCCCCEEEEEC--CCEEEECCCCCEECCCHHHHHHCCCC-------------CCCCCCCCCCEEEEEEECCCEEEEEECCCCCCEEEC-CHHHHCCC

>P1;d3n6wa1
CCCCEEEEEEECCCCEEEEEECCCCEEEEEHHHHHHCCCCCCCEECCCCEECCCHHHCCCCCCCCEEEEC--CCEEEECCCCCEEEECHHHHHHCC--
PSA

>P1;d3luua-
56642663344b--640103043a430505043012313a-------------99588268130571463ab700304043b6a03051-20170297

>P1;d3n6wa1
645404504248b25303030337650404043012203498035995854418aa61779010570837--630203048725040618302845--


Translating the sequences
CCCC**EEEEEC--C*EEEE*CCCCEE***HHHHHHCCCC-------------C***CCCCCCEEEEEEE**CEEEEEECCCC**EEE*-*HHHHC**
CCCCEEEEEEEC**CEEEEEECCCCEEEEEHHHHHHCCCC*************CHHHCCCCCC**EEEE*--C*EEEE*CCCCEEEE*H*HHHH*C--

310602.tem
_________________________________
CCCCEEEEEEEC--CEEEEEECCCCEEEEEHHHHHHCCCC-------------CHHHCCCCCCEEEEEEE--CEEEEEECCCCEEEEEH-HHHHHC--




Structural block scores
0	3	C	5.0	H	  5.2  4.8

4	10	E	4.4	M	  4.0  2.7

12	13	-	3.0	P	  75.0  6.8

15	20	E	4.3	M	  1.3  1.5

21	24	C	5.0	H	  5.4  4.8

25	29	E	3.8	M	  2.6  2.6

30	35	H	5.0	H	  1.7  1.7

36	39	C	5.0	H	  4.4  2.2

40	52	-	3.0	P	  75.0  5.4

54	56	H	3.0	P	  7.3  9.0

57	62	C	5.0	H	  4.7  4.2

63	69	E	4.1	M	  3.7  4.3

70	71	-	3.0	P	  11.0  75.0

73	78	E	4.3	M	  1.2  1.3

79	82	C	5.0	H	  6.1  5.2

83	87	E	3.8	M	  3.7  3.0

90	94	H	4.2	M	  2.0  3.4

96	97	-	3.0	P	  8.0  75.0

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