Reading input alignment file to find conserved blocks of secondary structure

The input structure based alignment from Comparer
_____________________________________________

>P1;d2hh6a1
CCCCCHHHHCCCCCCCHHHHHCCCHHHHHHHHCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHCCCCHHHHHCCCHHHHHHHC--CCC-CCCCCCCHHHHCC

>P1;d2o4ta1
--------------CCCHHHHCCCHHHHCCHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHCCCCHHHHHCCCHHHHHHHCCCCCCHHHHHCCHHHHC-C
PSA

>P1;d2hh6a1
9a8868a95473687374078059039203601557682116392156114600740470175a581351089836521793--c13-465787788869c

>P1;d2o4ta1
--------------b567366056048007068209730296982466126501740481274a5805710888145105822b967388869569888-8


Translating the sequences
**************CCHHHHHCCCHHHHHHHH******CCCCHHHHHHHHHHHHHHHHHHHHCCCCHHHHHCCCHHHHHHHC--CCC-****CC*HHHH*C
--------------CC*HHHHCCCHHHH**HHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHCCCCHHHHHCCCHHHHHHHC**CCC*HHHHCCHHHH*-C

158560.tem
_________________________________
--------------CCHHHHHCCCHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHCCCCHHHHHCCCHHHHHHHC--CCC-HHHHCCHHHHH-C




Structural block scores
0	13	-	3.0	P	  7.3  75.0

14	15	C	5.0	H	  5.0  8.2

16	20	H	4.6	H	  5.2  5.6

21	23	C	5.0	H	  4.7  3.7

24	37	H	3.9	M	  3.9  3.9

38	41	C	5.0	H	  2.5  4.2

42	61	H	5.0	H	  3.4  4.2

62	65	C	5.0	H	  7.1  6.9

66	70	H	5.0	H	  2.0  2.6

71	73	C	5.0	H	  8.3  8.0

74	80	H	5.0	H	  4.7  3.4

82	83	-	3.0	P	  75.0  6.8

84	86	C	5.0	H	  5.5  7.3

88	91	H	3.0	P	  5.5  7.5

92	93	C	5.0	H	  7.5  7.0

94	98	H	4.2	M	  7.4  7.8

>>>>>>