Reading input alignment file to find conserved blocks of secondary structure

The input structure based alignment from Comparer
_____________________________________________

>P1;d1z0jb1
-------------------CCCCCC-CHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHCCCCC--

>P1;d1z0kb1
CCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHCC-------CHHHHHHHHHHHHHHHHHHCCC
PSA

>P1;d1z0jb1
-------------------649904-40860486137db74823651761562154369a6b--

>P1;d1z0kb1
bb2919847bb83b381334152061207105847-------3583068145526515772876


Translating the sequences
-------------------******-*HHHHHHHC*******HHHHHHHHHHHHHHH****C--
*******************HHHHHH*HHHHHHH*C-------*HHHHHHHHHHHHHHHHHHC**

140125.tem
_________________________________
-------------------HHHHHH-HHHHHHHHC-------HHHHHHHHHHHHHHHHHHHC--




Structural block scores
0	18	-	3.0	P	  75.0  6.7

19	24	H	3.0	P	  5.3  3.0

26	33	H	4.5	M	  4.5  3.4

35	41	-	3.0	P	  7.7  75.0

42	60	H	4.5	M	  4.7  4.4

62	63	-	3.0	P	  75.0  6.5

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