Reading input alignment file to find conserved blocks of secondary structure The input structure based alignment from Comparer _____________________________________________ >P1;d2f2ha1 CEEEEECCCCCCCCCCCCCCCEEEEECCCCC--CEEEEEEECC-------CCCEEEEEEEEEE----CCEEEEEEEE---------CCCCCEEEECCCC-CCCEEC-----CEEEECCC------CCCEEEEC---CCCCCEEC--- >P1;d2g3ma4 CEEEEE-----------HHHEEEEEC--------CEEEEC----------CCC--CEEEEC------CCEEEEC-----------CCEEEEEEEEEC-CCCCCEEEECCCCEEECEEEE-----CCEEEEEEEEEECCEEEEE---- >P1;d2xvla5 CCEEEECCCCCCHH-HHCCCCEEEEEECC--CCEEEEEEECCCCCC-HHH-HCCEEEEEEEEECC--CCEEEECCCEEECCCCCC--CEEEEEEEECC------------------CCCCCCCCCCCCCEEEEEC-CCCEEEECCC- >P1;d3l4ya4 CEEEEEECCCCCHH-HHCCCCEEEEEECCCCCCEEEEEEECCCCCCCCCC-CCCCEEEEEEECC----CEEEEE-EEEE-CCCCCCCCEEEEEEEECCCCCCCCEEEECCEECCCCEEEEECCCCEEEEECCCEECCCCEEEEC--- >P1;d3weoa4 CCEEEECCCCCCHH-HHHCCCEEEEEECCCCCCEEEEEEECCCCCCCCCCCCCCCEEEEEEEEECCCEEEEEEE-EE-CHHHHHHCCCEEEEEEEEEECCCEEEC-----------------CCEEEEECCCCEECCCCCEEEEEEC PSA >P1;d2f2ha1 35051507398687263143030004a0769--5403050439-------8774201040428----a740506087---------5069130002a39-908607-----4064883a------40030517---84502032--- >P1;d2g3ma4 450624-----------bb4303067--------635561----------a48--050404------8720605-----------540402402033-897083020278651908548-----9510107063608530216---- >P1;d2xvla5 17051333938794-51421400000409--781754142128748-555-8732040206052a--612040370675089148--50803000147------------------a4a35844770b0672504-184440837a- >P1;d3l4ya4 2806241785a799-42352402040303a854083614113496a7177-7651030402057----740306-1526-527074b000540304808608b0603388852990618057a642030380703013401031--- >P1;d3weoa4 2a060416b2a8a8-633834040304028983063612015593a88229b4610204030737b96030107-05-568104749030130203216560546-----------------b635040470634007417120302 Translating the sequences CEEEEECCCCCC*****CCCCEEEEE*CCCC--*EEEEEE*CC-------CCC**EEEEEEEE----CCEEEEE*EE---------CC***EEEE*CCC-CCCEE*-----********------C**EEEEC---CCC**EEC--- CEEEEE-----------****EEEE*--------*EEEE*----------CCC--*EEEE*------CCEEEE*-----------CC*EEEEEEEEC-CCCCCEE**************-----CCEEEEEE*EE*CC*EEEE---- C*EEEECCCCCCHH-HHCCCCEEEEEECC--CCEEEEEEECCCCCC-***-*CC*EEEEEEEE**--CCEEEE***E********--CEEEEEEEECC------------------******CCCC***EEE*E*-CCCEEEEC**- CEEEEE*CCCCCHH-HHCCCCEEEEEECCCCCCEEEEEEECCCCCC****-CCC*EEEEEEE**----CEEEEE-EE**-*****CCCEEEEEEEECCCCCCC*E*****************CCC*EEEE**CEE*CCCEEEEC--- C*EEEECCCCCCHH-HH*CCCEEEEEECCCCCCEEEEEEECCCCCC****CCCC*EEEEEEEE******EEEEE-EE-*******CCCEEEEEEEE**CCC**E*-----------------CC**EEE***CEE*CCC*EEE**** 117125.tem _________________________________ CEEEEECCCCCCHH-HHCCCCEEEEEECCCCCCEEEEEEECCCCCC-***CCCC*EEEEEEEE*---CCEEEEE-EE-*-*****CCCEEEEEEEECCCCCCCEE*-----********---CCCCEEEEEECEE*CCCEEEEC--- Structural block scores 1 5 E 4.8 H 3.2 3.4 3.2 4.0 4.1 6 11 C 4.4 M 5.5 75.0 5.5 6.4 6.5 12 13 H 4.1 M 7.5 75.0 6.5 9.0 9.2 15 16 H 4.1 M 4.5 75.0 3.0 3.0 4.5 17 20 C 4.3 M 2.0 7.5 2.8 3.5 4.5 21 26 E 4.8 H 2.9 15.2 0.7 1.5 1.8 27 32 C 4.3 M 28.7 75.0 29.0 5.1 5.0 33 39 E 4.7 H 2.4 14.4 3.4 3.3 2.6 40 45 C 4.3 M 40.2 75.0 5.0 5.6 5.6 47 49 * 3.0 P 75.0 75.0 5.0 5.0 4.0 50 53 C 4.4 M 6.5 24.4 23.2 23.2 7.6 55 62 E 4.7 H 2.4 20.4 2.1 1.8 2.0 64 66 - 4.3 M 75.0 75.0 53.5 75.0 9.2 67 68 C 4.3 M 8.8 7.5 3.5 41.0 3.0 69 73 E 4.8 H 3.0 2.6 1.8 2.6 2.2 75 76 E 4.3 M 7.5 75.0 3.0 3.0 2.5 80 84 * 3.0 P 75.0 75.0 6.0 4.2 4.0 85 87 C 4.4 M 26.7 3.0 51.7 5.2 4.3 88 95 E 4.8 H 2.6 1.9 1.5 2.0 1.5 96 102 C 4.3 M 16.4 15.7 55.1 5.9 3.6 103 104 E 4.1 M 3.0 1.5 75.0 3.0 5.0 106 110 - 3.8 M 75.0 4.6 75.0 6.0 75.0 111 118 * 2.7 P 5.4 5.0 50.0 5.0 75.0 119 121 - 3.8 M 75.0 75.0 5.3 4.0 75.0 122 125 C 4.1 M 57.2 41.0 5.5 5.6 6.4 126 131 E 4.0 M 1.5 1.5 4.4 2.3 2.5 133 134 E 4.3 M 75.0 4.5 2.0 1.5 3.5 136 138 C 4.8 H 5.7 5.3 4.3 2.7 3.7 139 142 E 4.6 H 1.2 2.2 4.0 1.0 2.8 144 146 - 4.0 M 75.0 75.0 30.8 75.0 1.7 >>>>>>