Reading input alignment file to find conserved blocks of secondary structure The input structure based alignment from Comparer _____________________________________________ >P1;d1c3ga1 ------CEEEEEEEECHHHHHHCCEEEEEEEEEECC---CEEEEEEEEEECCCCCCCCCEEEECCCCCCCCC-CCCCCEEEEEEEECCCC---------------- >P1;d1c3ga2 CEEEECCEEEEEECCCHHHHHHC--EEEEEECCC-------CCEEEEEECC-CC-CCCCEEECCCCCCCCCCCCCCCCCEEEEECCCCCCCCCCCHHHHCC----- >P1;d1nlta1 --CCCCCCEEEEEEECCCHHHHC--EEEEEEEC--------CEEEEEEEC--CCCCCCCEEEECCCCCCC-C-CCCCCCEEEEEEECCCC---------------- >P1;d1nlta2 CCEEECCEEEEEEEEEHHHHHHC--CCCEEECCC-------CCEEECCCCCCCCCCCCCEEEECCCCCCCCCC-CCCCCEEEEEEEECCC---------------- >P1;d2q2ga1 ------CEEEEEEEECHHHHHHCEEEEEEEEEEEEECCEEEEEEEEEEEEECCCCCCCCEEEECCCCCCCCC-CCCCCEEEEEEEECCCC---------------- >P1;d2q2ga2 CCEEECCEEE-CEEEEHHHHHHC--EEEEEECCC-------CCEEEEEECC-CC-CCCCEEEECCCC-CCCCCCCCCCCEEEEEEEECCCCCCHHHHHHHHHHC-- >P1;d3agxa2 CCEEECCEEEEEEEEEHHHHHHC--EEEEEECCC-------CCEEEEEECC-CC-CCCCEEEECCCCCCCCCCCCCCCCEEEEEEEECCCCCCHHHHHHHHHHCCC PSA >P1;d1c3ga1 ------76463705025710960552336262703a---c4a46060407075b28473524285203366b-74614101010436a48---------------- >P1;d1c3ga2 61657b52010406054820680--083525045-------6962506397-40-74a3426375302427956872240204081872a92787576a6b----- >P1;d1nlta1 --a892a3355605025730880--34262528--------654150507--4b1756352528420886-9-6262220002034493a---------------- >P1;d1nlta2 71857c32021505075820560--871306146-------b86170608543046981425295401637a9-676240203041767a---------------- >P1;d2q2ga1 ------9445450504672198156361604051249a846745451504055b295735152862041955-b6922301020525a48---------------- >P1;d2q2ga2 6177592311-526053750471--150614067-------949261508a-60-769343516810-82a978b64120002060674a92778568748977-- >P1;d3agxa2 71666b23001106053940471--130602036-------955252508a-60-7681455166102547a4686322010206056488366a4566487658c Translating the sequences ------CEEEEEEEE*HHHHHHC**EEEEEE*****---****EEEEEE*C*CC*CCCCEEEECCCCCCCCC-CCCCC*EEEEEEE*CCC---------------- *****CCEEEEEE***HHHHHHC--EEEEEE*C*-------C*EEEEEECC-CC-CCCCEEE*CCCCCCCCC*CCCCCCEEEEE***CCC***********----- --***CC*EEEEEEE***HHHHC--EEEEEE*C--------C*EEEEEEC--CC*CCCCEEEECCCCCCC-C-CCCCCCEEEEEEE*CCC---------------- *****CCEEEEEEEE*HHHHHHC--***EEE*C*-------C*EEE***CC*CC*CCCCEEEECCCCCCCCC*-CCCCCEEEEEEE*CCC---------------- ------CEEEEEEEE*HHHHHHC**EEEEEE************EEEEEE***CC*CCCCEEEECCCCCCCCC-CCCCC*EEEEEEE*CCC---------------- *****CCEEE-*EEE*HHHHHHC--EEEEEE*C*-------C*EEEEEECC-CC-CCCCEEEECCCC-CCCC*CCCCCCEEEEEEE*CCC**************-- *****CCEEEEEEEE*HHHHHHC--EEEEEE*C*-------C*EEEEEECC-CC-CCCCEEEECCCCCCCCC*CCCCCCEEEEEEE*CCC**************** 49493.tem _________________________________ *****CCEEEEEEEE*HHHHHHC--EEEEEE*C*-------C*EEEEEECC*CC*CCCCEEEECCCCCCCCC*CCCCCCEEEEEEE*CCC***********----- Structural block scores 0 4 * 2.7 P 75.0 5.0 35.5 5.6 75.0 5.2 5.2 5 6 C 4.7 H 41.0 8.2 6.2 7.8 42.0 5.5 6.8 7 14 E 4.8 H 3.9 1.6 3.4 1.9 3.4 11.6 1.4 16 21 H 4.9 H 4.7 4.7 5.2 4.3 5.5 4.3 4.5 23 24 - 4.2 M 5.0 75.0 75.0 75.0 5.5 75.0 75.0 25 30 E 4.8 H 3.7 3.8 3.7 4.2 3.3 2.8 2.0 34 40 - 4.4 M 36.4 75.0 75.0 75.0 6.2 75.0 75.0 43 48 E 4.8 H 2.7 3.7 2.5 3.3 3.3 3.8 3.2 49 50 C 4.2 M 3.5 8.0 41.0 6.5 2.0 9.2 9.2 52 53 C 5.0 H 8.2 2.0 7.8 1.5 8.2 3.0 3.0 55 58 C 5.0 H 5.5 6.1 5.2 6.0 6.0 6.2 5.5 59 62 E 4.9 H 3.2 3.8 3.5 3.2 3.2 3.2 3.8 63 71 C 4.9 H 4.9 4.3 13.3 5.1 4.4 13.3 4.6 73 78 C 4.8 H 3.8 4.8 3.3 16.7 5.6 5.4 4.5 79 85 E 4.9 H 1.3 2.1 1.3 1.4 1.4 1.1 1.3 87 89 C 5.0 H 7.5 6.5 7.5 7.8 7.5 7.2 6.0 90 100 * 3.7 M 75.0 7.2 75.0 75.0 75.0 6.5 6.0 101 105 - 4.4 M 75.0 75.0 75.0 75.0 75.0 34.6 7.7 >>>>>>