Reading input alignment file to find conserved blocks of secondary structure The input structure based alignment from Comparer _____________________________________________ >P1;d1ffya2 CEEEEEEEECCCCCCCCCCHHHCCCCCCCEECCHHHCCCCCCCCCCCC-----CCCCCCCCCCCCCCCCCCCCHHHHCCCCCCCC-----CCCCCCCCCCCCCCCCCCCCCCCCC--CCCCCCCCCCCCCC-CCCCCCCCCCCCCHHHHCCCCCCCCCCCCCCC---------------CCCCCC--CCCCCCCCCCCHHHHCCHHHCCHHHHCCCCEEEEEEC >P1;d1h3na2 ---CEEEEEEEEECCC------CCCEEEEEECCHHHHHHCCEEEECCCCCHHHHCCC---HHH------HHHHHHHHHHHHHCCHHHHCCCCCCCCCEE----EEEEEECCCC---CCEEEEEECCCCCCCCCCCEEEECCCCCHHHHHHHHHHCCCCCCCEECCCCCCCCCCCCCCCCCCEECC---CHHHCCCCHHHHHH-HHHHHHHHCCCEEEEEEC--- >P1;d1wkaa- ----CEEEEEEEECCC----C---CEEEEEECCHHHHHHCCEEEECCCCC------------------------------------------------CCHHHCCCEEECCCC---CCEEEEEECCCCCCCCCCCEEEECCCCCHHHHHHHHHHCCCCCCCCCC---------------CCCCCCCCCCHHHCCCCHHHHHH-HHHHHHHHCCCEEEEEEC--- >P1;d1wnya- ----CCEEEEEEECCCHHHHCCCCEEEEEEECCHHHHHHCCEEEECCCCE----EEEEEECC-EEEEEEHHHHHHHHCC-----------CCCEEEEEEHHHHCCCCCCCCCCCCCCCCCCEEECCCCCCCCCCCCEEECHHHCHHHHHHHHHHCCCCCCCCCC---------------CCCCCCC----CCCCCCHHHHHH-HHHHHHHHCCCEEEEEC---- PSA >P1;d1ffya2 b73900101000106398028246021003132021020200001339-----53300036875401115904a60478083859-----9394743422371450103022919--710200518a1499-501140100023a725621562917800116a---------------732188--617606534447003830152046b060335665485 >P1;d1h3na2 ---543002020305c------5b440300142000000000000004171047002---992------7a60571154087368a4053ac5815002----0112030001---94501010021035b61200100000044700500542a0613200235c8606970670147504036---08715717064016-401720575920624337--- >P1;d1wkaa- ----b4210030405b----9---94040015300000001000023709------------------------------------------------515712b46010021---83304012064074994200300001149605600642a19535014a---------------675067a2019704826273027-400530474900152576--- >P1;d1wnya- ----6400001030552871808600000215501000000000012814----000033c9-1000003510481097-----------c16334516066036130400051b0a5011001183064881000400002259614810782903418023a---------------7340307----506854276027-5019405b491015364---- Translating the sequences *****EEEE****CCC******CCC****EECCHHH***CC****CCC-----********************HHHH********-----CCC**********CCC***CCCC**--C******CCCCCCC-CCC****CCCCC*HHHH*****CCCCCCCCCC---------------CCCCCC--*C***CCCC**HHHH**HHH**HH**C***EEE**** ---**EEEEEEEECCC------CCCEEEEEECCHHHHHHCCEEEECCCC********---***------****HHHH*************CCC******----******CCCC---CC***EEECCCCCCCCCCC*EEECCCCCHHHHHHHHHHCCCCCCC**C***************CC**CC---C***CCCCHHHHHH-HHHHHHHHCCCEEEEEE*--- ----*EEEEEEEECCC----*---CEEEEEECCHHHHHHCCEEEECCCC*------------------------------------------------*****CCC***CCCC---CC***EEECCCCCCCCCCC*EEECCCCCHHHHHHHHHHCCCCCCCCCC---------------CCCCCC***C***CCCCHHHHHH-HHHHHHHHCCCEEEEEE*--- ----**EEEEEEECCC******CC*EEEEEECCHHHHHHCCEEEECCCC*----********-**********HHHH**-----------CCC**********CCC***CCCC***CC***EEECCCCCCCCCCC*EEEC***CHHHHHHHHHHCCCCCCCCCC---------------CCCCCC*----**CCCCHHHHHH-HHHHHHHHCCCEEEEE*---- 50677.tem _________________________________ ---**EEEEEEEECCC******CCCEEEEEECCHHHHHHCCEEEECCCC*---********************HHHH********-----CCC**********CCC***CCCC**-CC***EEECCCCCCCCCCC*EEECCCCCHHHHHHHHHHCCCCCCCCCC---------------CCCCCC*-*C***CCCCHHHHHH-HHHHHHHHCCCEEEEEE*--- Structural block scores 0 2 - 4.3 M 7.2 75.0 75.0 75.0 3 4 * 2.2 P 4.5 4.5 43.2 40.5 5 12 E 4.6 H 0.4 1.2 1.8 1.0 13 15 C 5.0 H 3.0 5.8 5.5 3.3 16 21 * 3.3 M 4.8 75.0 64.0 4.3 22 24 C 4.3 M 3.3 6.8 53.0 4.7 25 30 E 4.5 M 1.2 1.3 1.5 0.5 31 32 C 5.0 H 2.5 3.0 4.0 5.0 33 38 H 4.7 H 0.8 0.0 0.0 0.2 39 40 C 5.0 H 1.0 0.0 0.5 0.0 41 44 E 4.3 M 0.2 0.0 0.0 0.0 45 48 C 4.8 H 22.5 1.2 3.0 3.0 50 52 - 4.3 M 75.0 1.7 75.0 75.0 53 72 * 3.0 P 3.2 36.4 75.0 9.4 73 76 H 4.3 M 5.1 3.5 75.0 3.2 77 84 * 3.2 M 6.0 5.1 75.0 58.2 85 89 - 4.3 M 75.0 4.5 75.0 75.0 90 92 C 4.3 M 7.0 9.3 75.0 6.5 93 102 * 2.2 P 3.7 31.6 39.4 3.4 103 105 C 4.3 M 3.0 0.7 5.8 3.3 106 108 * 1.0 P 1.3 1.7 2.3 2.3 109 112 C 5.0 H 3.2 0.2 0.8 1.2 113 114 * 3.5 M 5.0 75.0 75.0 6.2 116 117 C 4.7 H 41.0 6.5 5.5 7.8 118 120 * 1.0 P 1.0 2.0 2.3 0.7 121 123 E 4.3 M 1.7 0.3 1.0 0.3 124 134 C 4.9 H 11.2 2.9 4.1 3.5 136 138 E 4.3 M 1.7 0.3 1.0 1.3 139 143 C 4.6 H 1.0 0.8 1.2 1.8 144 153 H 4.6 H 4.7 2.7 3.8 4.6 154 163 C 4.9 H 4.3 2.8 4.9 4.0 164 178 - 4.3 M 75.0 5.2 75.0 75.0 179 184 C 4.8 H 4.8 3.0 5.2 2.8 189 191 * 1.4 P 4.3 5.3 5.3 26.7 192 195 C 5.0 H 4.5 5.0 5.0 5.8 196 201 H 4.8 H 3.0 2.8 3.5 4.0 203 210 H 4.7 H 2.6 3.2 2.9 4.4 211 213 C 4.5 M 5.8 5.3 4.3 4.7 214 219 E 4.5 M 3.8 3.0 3.3 3.2 221 223 - 4.3 M 5.7 75.0 75.0 75.0 >>>>>>