Reading input alignment file to find conserved blocks of secondary structure The input structure based alignment from Comparer _____________________________________________ >P1;d2ayua1 CCCCCCCHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHH-HHHHHCCCHHHC--CCCCCCCCCCCCHHHHHHHCC-CCHHHCCCHHHHCHHHHEEEEECCCC-CCCCCEEEEEEEECCCCCCCCC--CCEEEEEEEEECCCCC-----CCCCEEEEEEECCCCCCCCCCCCCEEEEECCCCCEEEEECCCHHHHHCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHCHHHHHHHC >P1;d5gpla- ----------------------------CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHC-------------------------------------CCCCHHHHHHHHCCHHHHCCCCHHHHHHHCCEEEEEEECCCCCCCCCEEEEEEEC--CCCCCCHHHCEEEEEEEEEEEEEECCCCCEEEEEEEEECCCCCCCCC-CCCCCCC---CCCC------CCCHHHHHHCCCCCC------------CCCCCHHHHHHHHHHCCCCCHHHHHHHHHHHHHHC >P1;d5x7va- --------------------------CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHC-------------------------------------CCCCHHHHHHCCC-HHHC-CCCCHHHHHHCCEEEEEEEC-CCCCCCCEEEEEEECHHHHHCCC---CEEEEEECCCC---------------CCCCEECCCCCC-CCCCCCC------------CCCCHHHHCCC-------------------CCCCCCHHHHHHHHCCCCCHHHHC--------- >P1;d6k02a1 -------CCCCCHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHCCCCCCCCCHHHHHHHHCCCCCCCCCCCCCCHHHHHHHHC-HHHHHHCCHHHHHHHCCEEEEEEEEE-C--CCEEEEEEEEC--CCCCCC--CCEEEEEEEEECCCCCCCHHHCCCCEEEEEECCCCCCCC-CCCCCEE-----C-----CEECCHHHHHCCCC------------HHHHHHHHHHHHHHHHHHCCCCCHHHHHCCCCC----- >P1;d7mtoa1 -----------------CCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHC-------------------------------------CCCCHHHHHHHCC-CCCHHHCCHHHHHHHCCEEEEEEEEC-CCCCCCEEEEEEEC--CCCCCC--CCEEEEEEEECC---------CCC---EEEEECCCCCCC-CCCCCCC-------------CCCHHHHHHCCC----------------CCCCC-HHHHHHHHCCCCCCHHHHCCC-----CC PSA >P1;d2ayua1 69875986779668947a269744774777776476649845661463056436405553571631232130727347a545672-751774917743--8bb3ab871363001300340-43028214b40270043040040302-6ba730020104033a603006--2730201020257019-----837142430602805055554202041646786735367390004008006783a8857882553676275015004101530026082031210483497 >P1;d5gpla- ----------------------------9895677666857667987628725553765657247136706-------------------------------------84a40002005209a20650148503600540200104213a9204003010305--6160037832404030507556664c778466645220a52a05038-c351119---7787------81100000402264b------------91607035004100630024057127724877777 >P1;d5x7va- --------------------------97a865747757787877788846666564874668357206606-------------------------------------8282000400450-7404-60065026004305201052-62488800302040588056106---1503020339a---------------a3055020905a-c340374------------b4100020037-------------------a1c333002202650095066237--------- >P1;d6k02a1 -------e8aa7396468268843764777586526606840773484046436529667772571323031669388a57674638c27aa626845869aa699771382000400430-84028405940240034030041505-7--93004020205--a05107--2830303020307069943380a024156050380613b-c441146-----8-----67610002008059------------a88672562141041006300260640314345----- >P1;d7mtoa1 -----------------878855655666666667656578866767846652643664667186216607-------------------------------------7386000300430-76038509a40360043054010433-58545103000306--804005--17302020336a---------856---42060490713b-c42117a-------------88100210673b----------------70472-800510164004706412678-----aa Translating the sequences ******************C*HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH***************-************--********CCCCHHHHHHHCC-**HHHCCCHHHH*HH**EEEEE**CC-CCCCC*EEEEEEEC**CCCCCC--CCEEEEEEEEEC****-----CCC*EEEEEEECCCCCCC*CCCCC*******C*******CCCHHHHHCCCC********************HHHHHHHHHHCCCCCHHHHH*C*******C ----------------------------*HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHC-------------------------------------CCCCHHHHHHH*C*HHHH*CCCHHHHHHHCCEEEEEEECC*CCCCCCEEEEEEEC--CCCCCC***CEEEEEEEEE**************EEEEE**CCCCCCC-CCCCCCC---**C*------CCCHHHHH*CCC***------------**CCCHHHHHHHHHHCCCCCHHHHH*********C --------------------------*HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHC-------------------------------------CCCCHHHHHH*CC-HHH*-CCC*HHHHHHCCEEEEEEEC-*CCCCCCEEEEEEEC*****CCC---CEEEEEE***C---------------****E*CCCCCC-CCCCCCC------------*CCCHHHH*CC-------------------CCC***HHHHHHH*CCCC*HHHHC--------- -------***********C*HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHC*************************************CCCCHHHHHHH*C-HHHHH*CCHHHHHHHCCEEEEEEE**-C--CC*EEEEEEEC--CCCCCC--CCEEEEEEEEEC*********CCC*EEEEEE*CCCCCCC-CCCCC**-----C-----***CCHHHHHCCCC------------********HHHHHHHHHHCCCCCHHHHHCC***----- -----------------*C*HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHC-------------------------------------CCCCHHHHHHHCC-***HH*CCHHHHHHHCCEEEEEEE*C-CCCCCCEEEEEEEC--CCCCCC--CCEEEEEEEE*C---------CCC---EEEEECCCCCCC-CCCCCCC-------------CCCHHHHH*CCC----------------*CCC*-HHHHHHHHCCCCC*HHHHCC*-----*C 143113.tem _________________________________ -----------------*C*HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHC-------------------------------------CCCCHHHHHHHCC-HHHHHCCCHHHHHHHCCEEEEEEECC-CCCCCCEEEEEEEC--CCCCCC--CCEEEEEEEEEC****-----CCC*EEEEEEECCCCCCC-CCCCCCC-----C------*CCCHHHHHCCCC---------------**CCCHHHHHHHHHHCCCCCHHHHHCC***---*C Structural block scores 0 16 - 4.1 M 7.1 75.0 75.0 35.5 75.0 20 69 H 4.9 H 4.8 16.8 14.4 4.9 5.5 71 107 - 3.9 M 11.6 75.0 75.0 6.8 75.0 108 111 C 5.0 H 3.2 6.6 5.0 3.5 6.0 112 118 H 4.9 H 1.0 1.0 1.1 1.1 1.0 119 120 C 4.4 M 2.0 1.0 2.5 1.5 1.5 122 126 H 4.1 M 3.4 4.7 18.0 4.4 4.8 127 129 C 4.6 H 2.3 1.7 2.0 3.0 4.7 130 136 H 4.9 H 3.5 3.1 2.7 2.7 3.4 137 138 C 4.5 M 3.5 4.5 3.5 3.5 3.5 139 145 E 4.9 H 1.6 1.0 1.9 1.9 2.0 146 147 C 3.9 M 1.0 1.5 38.5 2.5 3.0 149 154 C 4.6 H 6.3 4.2 5.0 28.2 4.7 155 161 E 5.0 H 1.0 1.0 1.3 1.1 0.9 163 164 - 3.8 M 6.8 75.0 8.0 75.0 75.0 165 170 C 4.8 H 2.5 2.7 3.0 3.9 2.8 171 172 - 4.5 M 75.0 7.5 75.0 75.0 75.0 173 174 C 4.5 M 4.5 2.5 38.0 5.0 4.0 175 183 E 4.8 H 1.1 2.6 2.8 1.6 2.1 185 188 * 3.0 P 4.2 5.8 75.0 5.5 75.0 189 193 - 3.8 M 75.0 7.7 75.0 5.4 75.0 194 196 C 4.1 M 6.0 5.3 75.0 3.5 6.3 198 204 E 4.2 M 2.7 4.1 24.8 3.0 23.1 205 211 C 4.9 H 3.6 4.1 3.8 4.6 5.1 213 219 C 4.7 H 2.4 4.6 4.8 4.6 5.4 220 224 - 4.2 M 4.8 47.8 75.0 75.0 75.0 226 231 - 4.3 M 5.0 63.7 75.0 63.5 75.0 233 235 C 4.8 H 4.0 3.3 1.7 2.3 5.7 236 240 H 4.9 H 0.8 0.0 0.4 0.4 0.6 241 244 C 4.5 M 3.5 2.0 40.0 5.5 6.9 245 259 - 4.2 M 6.2 61.4 75.0 61.8 75.0 260 261 * 2.5 P 6.5 5.0 75.0 6.5 41.0 262 264 C 3.8 M 4.7 4.3 8.0 4.3 3.7 265 274 H 4.7 H 1.7 1.9 2.1 1.9 9.8 275 279 C 4.9 H 2.2 1.8 3.8 2.2 3.0 280 284 H 4.8 H 2.6 3.0 3.4 2.6 2.6 285 286 C 3.9 M 1.5 7.0 41.0 2.5 6.5 287 289 * 2.7 P 1.7 4.7 75.0 4.0 52.7 290 292 - 3.8 M 5.0 7.0 75.0 75.0 75.0 >>>>>>