Reading input alignment file to find conserved blocks of secondary structure The input structure based alignment from Comparer _____________________________________________ >P1;d2ixma1 -----------CCCCEECCCCCHHHHHHHCCHHHHHHHHHHHHHHHHCCCC-CCCCCCC-C-CHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHCCCCCCCCCEECHHHHHHHHHHHHHHHHCCCCC-HHHHHHHHHCHHHHHHHHHHHHHHHCCCEECCCCHHHCCCCCCCHHHHHHHHHCCCCC---CCCHHHHHCHHHHHHHHHHCHHHHHHHHHHHHCC-CCHHHHCHHHHHHCC-CCCHHHHHHHHHHHHHHHCCCCHHHHCCCEECC-CCCCCCCCC >P1;d2ixna1 --------------CCCCC-CCCCCHHHHCCHHHHHHHHHHHHHHHCCCCC-CCCCCCCCC-CHHHHHHHHHHHHHHHHHCCCCCCC---CCCCCHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHCCCCCCCCCEECHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHCHHHHHHHHHHHHHHHHCCEECCCCCCCCCCCCCCHHHHHHHHHCCCCC---CCCHHHHHCHHHHHHHCCCCHHHHHHHHHHHHCCCCCHHHHCHHHHHHCC-CCCHHHHHHHHHHHHHHHCCCCHHHHCCCCCCC-CCCC----- >P1;d2ixoa1 CCCCCCCCCCCCCCCCCCCCCHHHHHHHHHCHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHCCCCCCCCCC---CCCCHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHCCCCCCCCCEECHHHHHHHHHHHHHHHHCCCCC--CCCHHHHHHHHHHHHHHHHHHHHHCCCEEC------CCCCCCCHHHHHHHHHCCCCHHHCCCCHHHHHCHHHHHHHCCCCHHHHHHHHHHHHCC-CCHHHHCHHHHHHHCCCCCHHHHHHHHHHHHHHHCCCCHHHHCCCCCCCCCCCCCCC-- PSA >P1;d2ixma1 -----------3790642067a81163057020132018104500770442-5185a18-3-581064017006202510761635b196970160047017505830581056005a83680150001002300033950001121001000000001314007-9602200004002200500130052060412766778301110000000000001a18---605060015870066218300003001102643a-871381143047108-364046006402720354003436103402004-101257489 >P1;d2ixna1 --------------16470-6774189059170177017002200520423-216534894-3920420270063036006626498---78135104601510362067007610680698306100200110001574010104100000000000331a10738701000002001101700130083050432951b95200410000000000001618---8050610478a30861273000030022038618b570581023025108-3a6046007502820564002225003500007-0067----- >P1;d2ixoa1 5446072682806806340759701650260200400340063007200612807394950b19104601800450170076074697---9005004600720574036105600388136004003200020000485010123100000000000100a106--a07030001003300700140063050553------c01400000000000002631890303084035674068247200001000101642a-57168205402710462750350078018304650054362034040060000167b-- Translating the sequences -----------CCCC**CCCCCHHHHHHHCCHHHHHHHHHHHHHHHHCCCC-CCCCCCC-C-CHHHHHHHHHHHHHHHHH*CCCCCCC**CCCCCHHHHHHHHHHHHHHHHHH**CCHHHHHHHHHHHHHHHCCCCCCCCCEECHHHHHHHHHHHHHHHHCCCCC-HHHHHHHHHCHHHHHHHHHHHHHHHCCCEECCCC***CCCCCCCHHHHHHHHHCCCCC---CCCHHHHHCHHHHHHH***CHHHHHHHHHHHHCC-CCHHHHCHHHHHHCC-CCCHHHHHHHHHHHHHHHCCCCHHHHCCC**CC-CCCCCCC** --------------CCCCC-CC***HHHHCCHHHHHHHHHHHHHHH*CCCC-CCCCCCCCC-CHHHHHHHHHHHHHHHHHCCCCCCC---CCCCCHHHHHHHHHHHHHHHHHHHHCC***HHHHHHHHHHHHCCCCCCCCCEECHHHHHHHHHHHHHHHHCCCCC*HHHHHHHHHCHHHHHHHHHHHHHHH*CCEECCCC***CCCCCCCHHHHHHHHHCCCCC---CCCHHHHHCHHHHHHHCCCCHHHHHHHHHHHHCC*CCHHHHCHHHHHHCC-CCCHHHHHHHHHHHHHHHCCCCHHHHCCCCCCC-CCCC----- ***********CCCCCCCCCC*HHHHHHH*CHHHHHHHHHHHHHHHH*CCC*CCCCCCCCC*CHHHHHHHHHHHHHHH**CCCCCCCC---CCCCHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHCCCCCCCCCEECHHHHHHHHHHHHHHHHCCCCC--***HHHHH*HHHHHHHHHHHHHHHCCCEEC------CCCCCCCHHHHHHHHHCCCC****CCCHHHHHCHHHHHHHCCCCHHHHHHHHHHHHCC-CCHHHHCHHHHHH*C*CCCHHHHHHHHHHHHHHHCCCCHHHHCCCCCCC*CCCCCCC-- 140984.tem _________________________________ -----------CCCCCCCCCCCHHHHHHHCCHHHHHHHHHHHHHHHHCCCC-CCCCCCCCC-CHHHHHHHHHHHHHHHHHCCCCCCCC--CCCCCHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHCCCCCCCCCEECHHHHHHHHHHHHHHHHCCCCC-HHHHHHHHHCHHHHHHHHHHHHHHHCCCEECCCC***CCCCCCCHHHHHHHHHCCCCC---CCCHHHHHCHHHHHHHCCCCHHHHHHHHHHHHCC-CCHHHHCHHHHHHCC-CCCHHHHHHHHHHHHHHHCCCCHHHHCCCCCCC-CCCCCCC-- Structural block scores 0 10 - 4.0 M 75.0 75.0 4.7 11 21 C 4.4 M 5.0 30.1 4.4 22 28 H 4.6 H 3.4 4.9 3.0 29 30 C 4.5 M 3.5 5.0 3.0 31 46 H 4.9 H 2.6 2.6 1.9 47 50 C 4.8 H 2.5 2.2 1.8 52 60 C 4.9 H 12.9 4.7 5.0 63 79 H 4.9 H 2.5 2.6 2.7 80 87 C 4.8 H 5.1 14.5 5.8 88 89 - 4.0 M 7.5 75.0 75.0 90 94 C 4.8 H 4.6 4.8 17.8 95 114 H 4.9 H 3.2 2.8 2.8 115 116 C 5.0 H 2.5 3.0 1.5 117 131 H 4.8 H 3.0 2.9 2.3 132 140 C 5.0 H 2.6 2.0 2.1 141 142 E 5.0 H 0.0 0.5 0.5 144 159 H 5.0 H 0.6 0.7 0.4 160 164 C 5.0 H 2.4 3.9 3.5 166 174 H 4.6 H 2.1 1.8 10.6 176 190 H 5.0 H 1.3 1.7 1.8 191 193 C 4.7 H 2.0 1.7 1.7 194 195 E 5.0 H 2.5 3.5 5.0 196 199 C 4.2 M 5.2 4.2 57.0 200 202 * 2.7 P 7.3 8.5 75.0 203 209 C 5.0 H 0.9 1.0 2.5 210 218 H 5.0 H 0.0 0.0 0.0 219 223 C 4.8 H 4.1 3.2 2.4 224 226 - 4.0 M 75.0 75.0 5.7 227 229 C 5.0 H 3.7 4.3 2.0 230 234 H 5.0 H 1.4 2.2 3.0 236 242 H 5.0 H 4.1 5.2 4.7 243 246 C 4.2 M 3.0 3.0 3.2 247 258 H 5.0 H 1.4 2.0 1.1 259 260 C 5.0 H 6.8 4.5 6.2 262 263 C 5.0 H 7.5 6.0 6.0 264 267 H 5.0 H 3.2 3.5 4.2 269 274 H 5.0 H 3.2 2.2 3.2 275 276 C 4.5 M 4.0 4.0 2.0 278 280 C 5.0 H 4.3 6.5 4.7 281 295 H 5.0 H 2.9 3.3 3.3 296 299 C 5.0 H 1.8 1.0 2.2 300 303 H 5.0 H 2.5 1.8 2.8 304 310 C 4.7 H 1.9 2.1 2.4 312 318 C 4.6 H 2.9 34.0 3.6 319 320 - 4.0 M 8.5 75.0 75.0 >>>>>>