Reading input alignment file to find conserved blocks of secondary structure The input structure based alignment from Comparer _____________________________________________ >P1;d1lsha2 -----------CCCCEEEEEEEEEEEEEECCCCCCEEEEEEEEEEEEEEECCCCEEEEEEEEEEEEEE-----EEECCCCCEEECCCCCHHHHHHHCCCEEEEEECCEEEEEECCCCCCHHHHHHHHHHHHHCCCCCCCCCCEEEEEEEECCEEEEEEEEEEECCC---CCEEEEEEEEEEEEEEEECC-CCCCCCCCC-----CCHHHHHH-----CCC---EEEEEEEEEEEEEECCEEEEEEEEEEEEEEECC------CCHHH-------------CCEEEEEEEEEEEEE----EEECC---------------------------------------------------------CCCCCCCC-------CCCCCCCCCCC--- >P1;d1lsha3 CCCCEEEEEEEEECCCCEEEEEEEEEEEE-CCEEEEEEEEEEEEEEEC----C---EEEEEEEEEEECHHHHHHHCC--CCCCCC---------CCCCEEEEEEECCEEEEEEEECCCCCHHHHHHHHHHH----------CCEEEEEEE---EEEEEEEEEEEECCCCCEEEEEEEEEEEEEEEEEEEEECC------CCCCCCCHHHHCCCCEEEEEEEEEEEEEEEEEEEEEECC-CCEEEEEEEEEEEEEEEEEEEEEEECCCCEEEEEECCCCCCEEEEEEEEEEEEEEEECCEEEEEECCCCCCCCHHHHHHCCCCCCCEEEEECCEECCCCEEEEEEEEEEECCCCCCCHHHHCCEEEEEEEEEECCCCCCCCEEEEEECCCC PSA >P1;d1lsha2 -----------054830030205215053636784705371040401020169720103036051230-----6241749125629ab39923820332000306a1607401026a0635000400400000003047a696063201024030203041783a8---a7114030506046075316-75aa69a89-----74776388-----235---540604060402449292003105041322406------86396-------------a15051341503047----36729---------------------------------------------------------b7a38027-------65154023434--- >P1;d1lsha3 86855565757478657424141551600-96354222225243334a----b---92615316074211406752c--989977---------841223233247484576844288a4aa157506624----------832564747---6354557463473a78431041532506244536240509------a04ba175831632924231525645434315171424a-864434012445433664823335147632431136146844314433060140532789354832056889b9989387153033576562774aa542250431430002246a347346004330330132787748335747384ab Translating the sequences -----------**CCEEEEEEEEEEEEEE*CC***EEEEEEEEEEEEE****C***EEEEEEEEEEEE-----EEEC**CCEEEC*********HHCC*EEEEEECCEEEEEE**CCCCHHHHHHHHHHHH**********CEEEEEEEE***EEEEEEEEEE**C---C*EEEEEEEEEEEEEEEE**-*CC******-----CCHHHHHH-----***---EEEEEEEEEEEEEEC*EEEEEEEEEEEEEEE**------**HHH-------------**EEEEEEEEEEEEE----EEE**---------------------------------------------------------C*******-------CCCC******C--- ***********EECC**EEEEEEEEEEEE-CCEEEEEEEEEEEEEEE*----C---EEEEEEEEEEE*********C--CC***C---------**CCEEEEEEECCEEEEEEEECCCC*HHHHHHHHHHH----------C*EEEEEEE---EEEEEEEEEEEEC***CEEEEEEEEEEEEEEEEEEE*ECC------*****CCHHHH*******EEE***EEEEEEEEEEEEE*C-**EEEEEEEEEEEEEEE******EE****************EEEEEEEEEEEEEEE****EEEEE*********************************************************CEEEEEEE*******CCCCEEEEEEC*** 56968.tem _________________________________ -----------EECCEEEEEEEEEEEEEE-CCEEEEEEEEEEEEEEEE----C---EEEEEEEEEEEE-----EEEC--CCEEEC---------HHCCEEEEEEECCEEEEEEEECCCCHHHHHHHHHHHH----------CEEEEEEEE---EEEEEEEEEEEEC---CEEEEEEEEEEEEEEEEEEE-ECC-----------CCHHHHHH-----EEE---EEEEEEEEEEEEEEC-EEEEEEEEEEEEEEEEE------EEHHH-------------EEEEEEEEEEEEEEE----EEEEE---------------------------------------------------------CEEEEEEE-------CCCCEEEEEEC--- Structural block scores 0 10 - 3.0 P 75.0 6.1 11 12 E 3.0 P 2.5 5.5 13 14 C 5.0 H 6.0 7.0 15 28 E 4.7 H 2.1 3.2 30 31 C 5.0 H 4.5 7.5 32 47 E 4.5 M 3.2 3.5 48 51 - 3.0 P 2.2 75.0 53 55 - 3.0 P 3.0 75.0 56 67 E 4.8 H 2.0 3.8 68 72 - 3.0 P 75.0 2.4 73 75 E 3.0 P 4.0 4.7 77 78 - 3.0 P 5.5 75.0 79 80 C 5.0 H 5.0 8.5 81 83 E 3.0 P 4.3 8.3 85 93 - 3.0 P 7.2 75.0 94 95 H 3.0 P 1.0 6.0 96 97 C 5.0 H 3.0 1.5 98 104 E 4.7 H 1.6 2.7 105 106 C 5.0 H 5.8 5.5 107 114 E 4.5 M 2.5 5.8 115 118 C 5.0 H 5.6 7.1 119 130 H 4.8 H 1.3 5.1 131 140 - 3.0 P 3.0 75.0 142 149 E 4.8 H 2.2 4.8 150 152 - 3.0 P 2.0 75.0 153 164 E 4.7 H 3.5 4.9 166 168 - 3.0 P 75.0 8.5 170 188 E 4.7 H 3.1 3.2 191 192 C 5.0 H 7.8 4.5 193 203 - 3.0 P 38.9 44.2 204 205 C 5.0 H 5.5 4.0 206 211 H 4.3 M 6.5 4.3 212 216 - 3.0 P 75.0 3.8 217 219 E 3.0 P 3.3 3.0 220 222 - 3.0 P 75.0 4.3 223 236 E 4.9 H 2.8 3.4 239 255 E 4.5 M 2.5 3.9 256 261 - 3.0 P 75.0 3.8 262 263 E 3.0 P 7.0 3.0 264 266 H 3.0 P 6.0 5.7 267 279 - 3.0 P 75.0 3.5 280 294 E 4.7 H 3.3 2.7 295 298 - 3.0 P 75.0 6.5 299 303 E 4.2 M 5.4 4.6 304 360 - 3.0 P 75.0 4.8 362 368 E 3.0 P 5.4 2.3 369 375 - 3.0 P 75.0 4.0 376 379 C 5.0 H 4.2 5.5 380 385 E 3.0 P 2.7 4.8 387 389 - 3.0 P 75.0 8.7 >>>>>>