Reading input alignment file to find conserved blocks of secondary structure The input structure based alignment from Comparer _____________________________________________ >P1;d1miwa1 CCCCCCCHHHHHHHCCCC--CHHHHHHHHCC---CCCHHHHHHHHHHH--HHHHHCCCCC---CCCCHHHCCCHHHHHHHHHHCCCCCCCCCCC--CCHHHHHHHHHCC--HHHCC---------CHHHHHHHHHHHCCCCCHHHHHHHCCCCHHHHHHHHHHH-HHHHHCC-------CHHHCCHHHHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHCCCCCCCHHHCCCCHHHHHHHHCCCCCCHHHHHHHHHHHHHHCCCCCCCHHHHHHHCCCCCHHHHHC >P1;d1ou5a1 CCCCCCCCCCCCCCCCCHHHHHHHHHHHCCCCCCCCCHHHHHHHHHCC--CCHHHCCCHHHHHHHHHHHCCCCHHHHHHHHHHCCCHHHHCCCCCCCCHHHHHHHHHHCCC------------CCCHHHHHHHHCCCC--CCCHHHHHHHCCCCCHHHHHHHHCCCCCCCCC--CCCCCCCCHHHHHHHHHCCCCCHHHHHHHHHHHHC--CHHHHHHHCCCCC------------------------------------------------------------------ >P1;d1vfga1 CCCCCCC-CHHHH-CCCHHHHHHHHHHHHC---CCCCHHHHHHHHHHHHCCHHHCCCHHHHHHHHHHHHHCCCHHHHHHHHHHCCCHHHHCCCCCCC-HHHHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHCCCCCCCCHHHHHHCCCCHHHHHHHHHH-HHHHHHHHHHHCCCCC--CCHHHHCC----HHHHHHHHHHHCCCH-HHHHHHHHHHHHHHHHCCC------------------------------------------------------------- PSA >P1;d1miwa1 5261aa713730553013--41013003505---80088037004600--5317817465---1226103054045001100505204422608--625a405905914--04608---------442020000030080a8165105616058a008402201-7208706-------7164043230050619201100001005457709632550573278030386b5030738103911b5875921881332004000256172568606620635655887b >P1;d1ou5a1 816186804204592202004002400762a83690586026004600--53049140640060034005595132003000816003301009595184057019308a2------------914200000000675--92035028206059623500200056306917--1198aa40630252168086861540010001011--4591066058296------------------------------------------------------------------ >P1;d1vfga1 6172a57-50054-2105004001301439---590297026206700b652055064a500900040042b4003002203506001201750805-761172044048116612642475506110000010028317a2036105308038204700522-35346300651572a8--a8268236----41941011011105a-8047413511631467797------------------------------------------------------------- Translating the sequences CCCCCCC**HHHH*CCC*--*HHHHHHHHCC---CCCHHHHHHHHHHH--*HHHHCCC**---****HHHCCCHHHHHHHHHHCCC****CCCC--CCHHHHHHHHH*C--HHH**---------CHHHHHHHHH**CCCCC*HHHHHHCCCCHHHHHHHHHH*-HHHHHCC-------C**HC*HHHHHH***HHHHHHHHHHHHHHC**CHHHHHHHHHHHC**CCC************************************************************* CCCCCCC*C*****CCCHHHHHHHHHHH*CC**CCCCHHHHHHHHH**--C*HHHCCCHHHHHHHHHHH*CCCHHHHHHHHHHCCCHHHHCCCCCCCCHHHHHHHHHHC**------------CCCHHHHHHHH*CCC--CCCHHHHHH*CCC**HHHHHHHH*******CC--*CCCCC**H*HHHHHHH*****HHHHHHHHHHHHC--CHHHHHHH****C------------------------------------------------------------------ CCCCCCC-CHHHH-CCCHHHHHHHHHHHHC---CCCCHHHHHHHHHHH**CHHH*CC*HHHHHHHHHHHHCCCHHHHHHHHHHCCCHHHHCCCCCCC-HHHHHHHHHH***HHH*********CC*HHHHHHHHHCCCCCCCCHHHHHHCCCCHHHHHHHHHH-*HHHHH*****CCCCC--*CHHHH**----HHHHHHHHHHH****-**HHHHHHHHHHH***CCC------------------------------------------------------------- 81891.tem _________________________________ CCCCCCC*CHHHH*CCCHHHHHHHHHHHHCC--CCCCHHHHHHHHHHH--CHHHHCCCHHHHHHHHHHHHCCCHHHHHHHHHHCCCHHHHCCCCCCCCHHHHHHHHHHC**HHH**-------CCCHHHHHHHHHCCCCCCCCHHHHHHCCCCHHHHHHHHHH**HHHHHCC--*CCCCC**HCHHHHHHH***HHHHHHHHHHHHHHC-*CHHHHHHHHHHHC**CCC------------------------------------------------------------- Structural block scores 0 6 C 5.0 H 6.0 5.4 5.5 9 12 H 4.0 M 3.8 2.8 2.2 14 16 C 5.0 H 1.3 1.3 1.0 17 28 H 4.6 H 14.2 2.1 1.8 29 30 C 4.5 M 2.5 6.2 42.0 31 32 - 4.0 M 75.0 5.5 75.0 33 36 C 4.8 H 20.8 5.0 4.0 37 47 H 4.8 H 3.3 2.9 3.5 48 49 - 4.0 M 75.0 75.0 8.8 51 54 H 4.5 M 4.8 4.0 3.0 55 57 C 4.7 H 4.0 1.7 3.3 58 69 H 4.2 M 20.9 2.3 2.7 70 72 C 5.0 H 3.0 6.3 5.8 73 82 H 5.0 H 1.6 1.7 1.5 83 85 C 5.0 H 2.3 2.3 2.0 86 89 H 4.0 M 2.5 1.5 0.8 90 97 C 4.6 H 21.8 3.8 12.6 98 107 H 4.9 H 4.8 3.7 3.2 109 110 * 2.7 P 75.0 6.2 4.5 111 113 H 4.0 M 3.3 75.0 4.3 114 115 * 2.7 P 4.0 75.0 1.5 116 122 - 4.0 M 75.0 75.0 4.7 123 125 C 4.0 M 51.3 4.7 2.3 126 134 H 4.9 H 0.9 0.2 0.2 135 142 C 4.4 M 3.8 22.4 4.2 143 148 H 5.0 H 3.8 3.3 3.0 149 152 C 4.8 H 3.0 2.8 2.8 153 162 H 4.8 H 3.5 2.7 3.0 163 164 * 2.7 P 38.0 2.5 39.0 165 169 H 4.0 M 4.8 4.8 4.2 170 171 C 4.0 M 3.0 4.0 0.0 172 173 - 4.0 M 75.0 75.0 5.5 175 179 C 4.2 M 61.4 7.8 6.5 180 181 * 2.7 P 3.5 2.0 75.0 184 190 H 4.4 M 2.4 3.4 14.6 191 193 * 2.7 P 2.3 4.7 75.0 194 207 H 4.6 H 1.6 1.9 2.1 212 222 H 4.6 H 4.3 4.6 3.3 224 225 * 2.7 P 4.0 75.0 6.5 226 228 C 4.0 M 2.0 75.0 7.7 229 289 - 4.0 M 4.4 75.0 75.0 >>>>>>