Reading input alignment file to find conserved blocks of secondary structure

The input structure based alignment from Comparer
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>P1;d1iv3a-
-----CEEEEEEEEEEEE---CCCEEECCEEECCCEEECCCCCCCHHHHHHHHHHHHCCCCCCHHHHCCCCCCCCCCCCHHHHHHHHHHHHHHCCCCEEEEEEEEECCCCCCHHHHHHHHHHHHHHHCCCHHHEEEEEECCCCC----CCCEEEEEEEEEEC---

>P1;d3f0da-
--CCEEEEEEEEEEEEEE---CCCEEECCEEECCCEEECCCCCCCHHHHHHHHHHHHHCCCCCHHHHCCC----CCCCCHHHHHHHHHHHHHHCCEEEEEEEEEEECCCCCCHHHHHHHHHHHHHHHCCCHHHEEEEEECCCCCHHHHCCCEEEEEEEEEEEEC-

>P1;d4c82a-
CCCCCEEEEEEEEEEEEECCCCCEEEECCEEEE-EEEECCCCCCCHHHHHHHHHHHHHHCCCCHHHHCC--------CHHHHHHHHHHHHHHHCCEEEEEEEEEEECCCCCCCCCHHHHHHHHHHHHCCCHHHEEEEEECCCCCHHHHCCCEEEEEEEEEEEECC
PSA

>P1;d1iv3a-
-----5715152525047---b4603002360705000429330000000002000400a1662b72036927716a47024004200620464a0804306050102519066259601310170060569308070650969----25530204040405---

>P1;d3f0da-
--7533819052327027---c260200017081920053302000001000200050082662761087----48727025105401630693704035040100053190862296035200700a056840505166489895006160010506030057-

>P1;d4c82a-
a6765280504242706145ab54010021609-603041b52000012000300080092762a6247--------8607610620350076470604604040201218069248701630173081749304041754978a6006360010304040433c


Translating the sequences
-----*EEEEEEEEEEEE---CCCEEECCEEECCCEEECCCCCCCHHHHHHHHHHHH*CCCCCHHHHCCC****CCCCCHHHHHHHHHHHHHHCC**EEEEEEEEECCCCCCHHHHHHHHHHHHHHHCCCHHHEEEEEECCCCC----CCCEEEEEEEEEE*---
--CC*EEEEEEEEEEEEE---CCCEEECCEEECCCEEECCCCCCCHHHHHHHHHHHHHCCCCCHHHHCCC----CCCCCHHHHHHHHHHHHHHCCEEEEEEEEEEECCCCCCHHHHHHHHHHHHHHHCCCHHHEEEEEECCCCCHHHHCCCEEEEEEEEEEEEC-
**CC*EEEEEEEEEEEEE***CC*EEECCEEE*-*EEECCCCCCCHHHHHHHHHHHHH*CCCCHHHHCC--------C*HHHHHHHHHHHHHHCCEEEEEEEEEEECCCCCC***HHHHHHHHHHHHCCCHHHEEEEEECCCCCHHHHCCCEEEEEEEEEEEEC*

69765.tem
_________________________________
--CC*EEEEEEEEEEEEE---CCCEEECCEEECCCEEECCCCCCCHHHHHHHHHHHHHCCCCCHHHHCCC----CCCCCHHHHHHHHHHHHHHCCEEEEEEEEEEECCCCCCHHHHHHHHHHHHHHHCCCHHHEEEEEECCCCCHHHHCCCEEEEEEEEEEEEC-




Structural block scores
0	1	-	4.0	M	  75.0  75.0  8.2

2	3	C	4.0	M	  75.0  6.0  6.5

5	17	E	4.9	H	  3.8  3.8  3.2

18	20	-	4.0	M	  75.0  75.0  6.5

21	23	C	4.7	H	  7.2  6.8  6.8

24	26	E	5.0	H	  1.0  0.7  0.3

27	28	C	5.0	H	  1.0  0.0  1.0

29	31	E	5.0	H	  3.0  2.7  2.3

32	34	C	4.0	M	  4.0  6.0  30.0

35	37	E	5.0	H	  0.0  0.7  1.0

38	44	C	5.0	H	  3.0  1.9  3.4

45	57	H	4.9	H	  0.5  0.6  1.1

58	62	C	4.8	H	  4.7  4.4  4.8

63	66	H	5.0	H	  5.6  4.0  5.1

67	69	C	4.7	H	  3.0  5.0  28.7

70	73	-	4.0	M	  6.2  75.0  75.0

74	78	C	4.2	M	  5.7  5.6  47.8

79	92	H	5.0	H	  2.1  3.0  3.1

93	94	C	5.0	H	  7.2  5.0  5.5

95	105	E	4.8	H	  2.5  1.5  2.4

106	111	C	5.0	H	  2.8  3.0  2.0

112	126	H	4.8	H	  3.1  3.3  3.8

127	129	C	5.0	H	  3.7  5.2  5.3

130	132	H	5.0	H	  6.0  6.0  5.3

133	138	E	5.0	H	  3.5  2.8  2.7

139	143	C	5.0	H	  5.8  7.0  6.6

144	147	H	4.0	M	  75.0  3.5  4.1

148	150	C	5.0	H	  4.0  4.3  5.0

151	162	E	4.8	H	  8.1  1.7  1.6

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