Reading input alignment file to find conserved blocks of secondary structure

The input structure based alignment from Comparer
_____________________________________________

>P1;d2a1va1
CCCCCCHHHHHHHHCCCCCEEEECCCCCCEEEEEEEECCEEEEEEEEECCCCCCEEEEECCHHHHHHHHHHCCCCEEECCCCCCCCEEEEECCCCCCHHHHHHHHHHHHHHHHHHHCCHHHHHHHCCCCCC

>P1;d2fkia1
----CCHHHHHHHHCCCCCCEEEEECCCCEEEEECC----CCEEEEECCCCCCCEEEECCCH-HHHHHHHHHCCCCCCCCCCCCCCCEEEECCCCCCHHHHHHHHHHHHHHHHHC-CCHHHHHHHHHC---
PSA

>P1;d2a1va1
54604619104510760440336435b65100020038a315300002365a4050002075930760386249006407816584001010346062920250036002300494089922971803981

>P1;d2fkia1
----0818503a3057254080664a6580220204----92200000168a6200005707-5046226878920455903779824002179007693046004300730257-068724561986---


Translating the sequences
****CCHHHHHHHHCCCCCEEEE**CCCCEEEEEEE****EEEEEEEECCCCCCEEEEECCH*HHHHHHHH*CCCEEECCCCCCCCEEEEECCCCCCHHHHHHHHHHHHHHHHHH*CCHHHHHHH**C***
----CCHHHHHHHHCCCCC*EEEEECCCCEEEEE**----**EEEEE*CCCCCCEEEE*CCH-HHHHHHHHHCCC***CCCCCCCC*EEEECCCCCCHHHHHHHHHHHHHHHHH*-CCHHHHHHHHHC---

142906.tem
_________________________________
----CCHHHHHHHHCCCCCEEEEEECCCCEEEEEEE----EEEEEEEECCCCCCEEEEECCH-HHHHHHHHHCCCEEECCCCCCCCEEEEECCCCCCHHHHHHHHHHHHHHHHHH-CCHHHHHHHHHC---




Structural block scores
0	3	-	3.0	P	  3.8  75.0

4	5	C	5.0	H	  5.0  4.0

6	13	H	5.0	H	  2.6  3.8

14	18	C	5.0	H	  4.2  4.6

19	24	E	4.0	M	  3.2  4.0

25	28	C	5.0	H	  6.9  7.4

29	35	E	4.4	M	  0.4  1.4

36	39	-	3.0	P	  6.1  75.0

40	47	E	4.2	M	  1.4  1.6

48	53	C	5.0	H	  4.8  5.6

54	58	E	4.6	H	  1.4  1.0

59	60	C	5.0	H	  3.5  3.5

63	71	H	4.8	H	  3.9  4.4

72	74	C	5.0	H	  4.3  6.3

75	77	E	3.0	P	  3.3  3.0

78	85	C	5.0	H	  4.9  6.0

86	90	E	4.6	H	  0.4  1.6

91	96	C	5.0	H	  3.2  4.0

97	114	H	4.9	H	  2.6  3.3

116	117	C	5.0	H	  4.0  3.0

118	126	H	4.6	H	  5.2  5.6

128	130	-	3.0	P	  6.0  75.0

>>>>>>