Reading input alignment file to find conserved blocks of secondary structure

The input structure based alignment from Comparer
_____________________________________________

>P1;d1z1wa3
-CCEEEEEEECCCEEEEEEEEECCC--------CEEECCCCEEEEEECC--C----------CEEEEEECC-CEEEE--CC------CCCEECHHHCCCCEEEEC-

>P1;d4fkea3
--CEEEEECCC--CCEEEEEECCCCCCCCCCCCCCCCCCCCEEECEEECCEE----------CCCEEECCCCEEEC---HHHCCCCCCCEEECHHHCCCCEEEECC

>P1;d4qmea3
CCCCEEEEECCCCEEEEEEEEECC--CCCCCCCC----CCEEEEEEECCCCEECEEECCEEECCEEEECCCCEEEEEEE---CCCCCCEEEECCCCCCCCEEEC--

>P1;d6q4ra3
--CEEEEEEEECCEEEEEEEECCCC---------CCCCCCCEEEEEEECCEE----------EEEEEEECCCEEEEE--CCCCCC---CEEECHHHCCCCEEEECC
PSA

>P1;d1z1wa3
-3200020754ca51204013339b--------9468083507010408--b----------92664505a-74217--0a------116500097849060647-

>P1;d4fkea3
--201040417--504040722397a95a399a2999323604020224585----------19415087576344---820516b92505002a8819060734b

>P1;d4qmea3
63513050702d720503050714--52989818----3130300042c565020319c44564250606775330504---508490803013c610706172--

>P1;d6q4ra3
--3020001366450504041378d---------c2c64370701020154a----------833725057664415--087709---605002a79280506447


Translating the sequences
-*CEEEEEE*CCCEEEEEEEE*CCC--------C***CCCCEEEEEE*C--*----------C*EEEE*CC-*EEEE--**------CC*EECHHHCCCCEEEEC-
--CEEEEE**C--**EEEEEE*CCC********C***CCCCEEE*EE*CC*E----------C**EEE*CCCEEE*---***CCC**CCEEECHHHCCCCEEEEC*
**C*EEEEE*CCCEEEEEEEE*CC--*******C----CC*EEEEEE*CC*E**********C*EEEE*CCCEEEEE**---CCC**C*EEEC***CCCCEEE*--
--CEEEEEE**CCEEEEEEEE*CCC---------***CCCCEEEEEE*CC*E----------**EEEE*CCCEEEEE--***CCC---CEEECHHHCCCCEEEEC*

254133.tem
_________________________________
-*CEEEEEE*CCCEEEEEEEE*CCC-*******C***CCCCEEEEEE*CC*E----------C*EEEE*CCCEEEEE--***CCC**CCEEECHHHCCCCEEEEC*




Structural block scores
3	8	E	4.8	H	  1.5  1.5  2.7  0.5

10	12	C	4.3	M	  9.0  52.3  7.5  5.3

13	20	E	4.8	H	  2.0  2.8  1.9  2.4

22	24	C	4.8	H	  7.8  6.3  26.7  9.5

26	32	*	3.5	M	  75.0  8.0  6.0  75.0

34	36	*	2.3	P	  6.0  9.0  75.0  9.0

37	40	C	4.7	H	  4.0  3.5  20.5  5.0

41	46	E	4.9	H	  2.0  1.3  1.2  1.7

48	49	C	4.7	H	  41.5  4.5  8.8  3.0

52	61	-	4.3	M	  75.0  75.0  4.0  75.0

64	67	E	4.8	H	  5.2  2.5  3.2  4.2

69	71	C	4.8	H	  30.2  6.3  6.7  6.0

72	76	E	4.6	H	  4.2  18.4  3.2  4.0

77	78	-	4.3	M	  75.0  75.0  2.0  75.0

79	81	*	2.7	P	  28.5  3.3  75.0  5.0

82	84	C	4.3	M	  75.0  4.0  4.3  5.3

85	86	*	3.5	M	  75.0  10.2  6.5  75.0

87	88	C	4.3	M	  1.0  3.5  4.0  40.5

89	91	E	4.8	H	  3.7  1.7  1.0  1.7

93	95	H	4.3	M	  5.3  6.8  7.2  6.5

96	99	C	5.0	H	  5.2  4.5  2.0  4.8

100	103	E	4.8	H	  4.0  4.0  4.0  3.8

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