Reading input alignment file to find conserved blocks of secondary structure The input structure based alignment from Comparer _____________________________________________ >P1;d1a3aa- --------------------------------------------------CCCCCH-HH----EECCCCCCCHHHHHHHHHHHHHHCCCCCC-HHHHHHHHHHH-------------------------------------HCCCEEE----CCEECCCC-CHHHHHHCCCCEEEEEEEEEEEEC-CCCC---CCEEEEEEEEECCC---CCHH-HHHHHHHHHCCCHHHHHHHHHCCCHHHHHHHCCCCC----------------------------------- >P1;d1a6ja- -----------------------------------------------CCHHHCCCH-HH----EEEEECCCCHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHC-------------------------------------CCCCEEE----CCEECCEEEE---CHHHCCCEEEEEEEEEEECCCCCCC----CCEEEEEEEEEEHHHCCCCH-HHHHHHHHHHCCHHHHHHHHHCCCHHHHHHHHHCCC----------------------------------- >P1;d3bjva- -----------------------------------------------CCHHHHHHHHCC----EEEEECCCCHHHHHHHHHHHHHHCCCCCC-HHHHHHHHHHHH-----------------------------------HCCCCCCCC----EEECCCCC---HHHCCCCCEECEEEEEEEEECCCC------CEEEEECCEECCC--HHHHHHCHHHHHHHHHCCCCHHHHHHCCCCHHHHHHHHHHHHHCHHHC----------------------------C >P1;d3lf6a- -----------------------------------------------CCCCCCCCH-HH----EEEECCCCCHHHHHHHHHHHHHHCCCCCC-CHHHHHHHHHHH-----------------------------------C-CCEECCCCC--EEECCCCC---C--CCCCC-EEEEEEEEEEEECCCCCCCCCEEEEEEEEEECCC--HHHCC--CCCHHHHHCC--CCCCHHHCC-CHHHHCCHHHHHC----------------------------------- >P1;d3oxpa1 -------------------------------------------------CCCCCCH-HH----EEEECCCCCHHHHHHHHHHHHHHCCCCCC-HHHHHHHHHHHH-----------------------------------HCCCCCCCC----CEE-CCCC---HHHCCCCCEEEEEEEEEEECCCCHH----HCCEEEEEEEECCC--HHHHH-HHHHHHHHHHCCHHHHHHHHCCCCHHHHHHHHCCC------------------------------------ >P1;d3urra1 -----------------------------------------------CCCCCCCCH-HH----EEEEECCCCCC-CHHHHHHHHHHHHCCCHHHHHHHHHHHCC--------------------------------------CCCEEE----CCEECCEEEC---C-CCCCCEEEEEEEEEEECCCCCCC----CCEEEEEEEEECCC--CCHH-HHHHHHHHHHCCHHHHHHHHHCCCHHHHHHHHHCCCC---------------------------------- >P1;d4ky9a- CEEEEEEEEECCCCCCEEEEEEEEECCCEEECCCCCCCCCCCCCCCCHHHHHHHHH-HHHCCEEEEEECCCCHHHHHHHHHHHHHHCCCCCH-HHHHHHHHHHCCCEECHHHHHHCCCCEECEECCCCCCCCCCCCCHHHHHHCCCCCCCCCCEEEEEEEEEC----CCCCCEEEEEEEEEEECCCCCCC---CCCEEEEEEEEECCCCCCCHH-HHHHHHHHHHHCHHHHHHHHHCCCHHHHHHHHHHHHHCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHCCC PSA >P1;d1a3aa- --------------------------------------------------809077-90----02174709626600510051038181046-60060015108-------------------------------------6750234----81000000-15914a405500000000280050-2989---a2302000000035---8416-702610681086861055005195394039106a2a----------------------------------- >P1;d1a6ja- -----------------------------------------------480370035-60----0404170a627500320061008109253850271036307-------------------------------------6800041----a000002160---879084000000003740909064b----54010000001036349816-702620373075982185038076455002000778----------------------------------- >P1;d3bjva- -----------------------------------------------350140075090----04073709614300420030036280057-603820163047-----------------------------------850300447----30000108---272105420000000573050558------4602000000044--993277403110200061970273028085485017006604a27518----------------------------b >P1;d3lf6a- -----------------------------------------------900d04045-50----02406771725600530050038260029-601730082067-----------------------------------8-200252940--00020106---2--40562-000000573270702aa78940602000010037--4a239--5081067005--810660262-7376032069219----------------------------------- >P1;d3oxpa1 -------------------------------------------------0693058-80----03036708504400420051027580057-601720184057-----------------------------------641400537----100-0316---48100453100000026006080ac----31603000000046--8a248-715540660194a901640260665a504700462------------------------------------ >P1;d3urra1 -----------------------------------------------705012024-70----0328261a517-00540041027338165840173048308--------------------------------------910031----6200003150---a-908811000010364080a0549----44010000000196--7408-5045303500648502550652754540252005166---------------------------------- >P1;d4ky9a- 100000100205655500000300029501001a1191165180805650151055-00640001141828605300440064028290046-70282015003160002b7078074172000294592848365470366109594786010000000005----20730000000048117070062---812010000000123760402-000000010013400262038076395027006412813275696b9759a65783765664245604759 Translating the sequences --------------------------------------------------**CCCH-HH----EE***CCCCHHHHHHHHHHHHHHCCCCC*-HHHHHHHHHH*-------------------------------------*CCC***----**EECC**-*******CCCCEEEEEEEEEEE*C-CCCC---*C*EEEEEEEE*CC---**HH-HHHHHHHHH*CCHHHHHHHH*CCCHHHHHHH*****----------------------------------- -----------------------------------------------*****CCCH-HH----EEEE*CCCCHHHHHHHHHHHHHH**CCC**HHHHHHHHHH*-------------------------------------*CCC***----**EECC****---****CCCEEEEEEEEEEE*CCCCCC----C*EEEEEEEE*********H-HHHHHHHHHHCCHHHHHHHH*CCCHHHHHHHHH***----------------------------------- -----------------------------------------------********H***----EEEE*CCCCHHHHHHHHHHHHHHCCCCC*-HHHHHHHHHH**-----------------------------------**CCC****----*EECC***---***CCCCCEE*EEEEEEEE*CCCC------C*EEEE**EE*CC--***HH**HHHHHHHHHCC**HHHHHH*CCCHHHHHHHHH*********----------------------------* -----------------------------------------------*****CCCH-HH----EEEE*CCCCHHHHHHHHHHHHHHCCCCC*-*HHHHHHHHH**-----------------------------------*-CC*******--*EECC***---*--CCCCC-EEEEEEEEEE**CCCCC******EEEEEEEE*CC--*****--***HHHHH*C--****HHH*C-CHHHH**HHH***----------------------------------- -------------------------------------------------***CCCH-HH----EEEE*CCCCHHHHHHHHHHHHHHCCCCC*-HHHHHHHHHH**-----------------------------------**CCC****----*EE-C***---***CCCCCEEEEEEEEEEE*CCC**----*C*EEEEEEEE*CC--***HH-HHHHHHHHHHCCHHHHHHHH*CCCHHHHHHHH***------------------------------------ -----------------------------------------------*****CCCH-HH----EEEE*CCCC**-*HHHHHHHHHH**CCC**HHHHHHHHH**--------------------------------------CCC***----**EECC****---*-CCCCCEEEEEEEEEEE*CCCCCC----C*EEEEEEEE*CC*--**HH-HHHHHHHHHHCCHHHHHHHH*CCCHHHHHHHHH****---------------------------------- *******************************************************H-HH****EEEE*CCCCHHHHHHHHHHHHHHCCCCC*-HHHHHHHHHH****************************************CC*********EE*******----CCCCCEEEEEEEEEEE*CCCCCC---*C*EEEEEEEE*CC*****HH-HHHHHHHHHH*CHHHHHHHH*CCCHHHHHHHHH************************************** 55804.tem _________________________________ -----------------------------------------------*****CCCH-HH----EEEE*CCCCHHHHHHHHHHHHHHCCCCC*-HHHHHHHHHH**-----------------------------------**CCC****---**EECC****--***CCCCCEEEEEEEEEEE*CCCCCC---*C*EEEEEEEE*CC*-***HH-HHHHHHHHHHCCHHHHHHHH*CCCHHHHHHHHH****---------------------------------- Structural block scores 0 46 - 4.6 H 75.0 75.0 75.0 75.0 75.0 75.0 2.3 47 51 * 1.8 P 46.6 4.4 2.6 4.5 33.0 2.6 3.4 52 54 C 4.2 M 5.3 1.0 2.3 2.7 2.7 1.3 2.0 57 58 H 4.6 H 4.5 3.0 4.5 2.5 4.0 3.5 0.0 59 62 - 4.6 H 75.0 75.0 75.0 75.0 75.0 75.0 2.5 63 66 E 4.8 H 2.5 2.0 2.8 1.5 1.5 3.2 1.5 68 71 C 5.0 H 5.5 5.9 5.5 5.5 5.0 5.6 6.0 72 85 H 4.9 H 2.6 2.4 1.9 2.6 2.1 7.6 2.6 86 90 C 4.7 H 2.8 3.4 3.0 2.0 3.6 4.2 3.0 93 102 H 4.9 H 1.9 2.7 2.9 2.7 2.9 3.0 2.5 103 104 * 2.0 P 41.5 41.0 5.5 6.5 6.0 41.5 2.0 105 139 - 4.6 H 75.0 75.0 75.0 75.0 75.0 75.0 4.0 140 141 * 2.8 P 40.5 40.5 6.5 41.5 5.0 75.0 6.0 142 144 C 4.7 H 4.0 2.7 1.0 0.7 1.7 3.3 3.3 145 148 * 1.5 P 21.0 20.0 3.8 4.5 3.8 19.8 6.2 149 151 - 4.3 M 75.0 75.0 75.0 26.3 75.0 75.0 4.7 152 153 * 2.0 P 4.5 5.2 39.0 37.5 38.0 4.0 0.5 154 155 E 5.0 H 0.0 0.0 0.0 0.0 0.0 0.0 0.0 156 157 C 4.4 M 0.0 0.0 0.0 1.0 37.5 0.0 0.0 158 161 * 1.7 P 19.0 2.2 21.0 20.5 21.2 2.2 0.0 162 163 - 4.4 M 7.0 75.0 75.0 75.0 75.0 75.0 40.0 164 166 * 2.9 P 5.2 30.0 3.7 50.7 4.3 53.5 75.0 167 171 C 4.8 H 2.8 4.2 2.4 3.4 2.4 5.2 2.4 172 182 E 4.9 H 0.9 1.3 1.4 8.4 0.8 1.4 1.3 184 189 C 4.6 H 17.2 5.1 28.0 5.0 17.7 4.8 2.5 190 192 - 4.6 H 75.0 75.0 75.0 8.0 75.0 75.0 75.0 196 203 E 4.9 H 0.2 0.1 0.2 0.4 0.4 0.1 0.1 205 206 C 4.6 H 4.0 1.5 4.0 5.0 5.0 5.0 1.5 209 211 * 1.5 P 29.0 7.0 7.0 5.5 6.8 28.7 3.3 212 213 H 4.4 M 3.5 3.5 4.5 6.0 6.0 4.0 1.0 215 224 H 4.7 H 3.1 3.0 1.1 10.2 3.5 2.5 0.1 225 226 C 4.6 H 7.0 6.0 3.5 40.0 6.5 5.0 2.0 227 234 H 4.7 H 3.1 4.5 3.8 12.2 4.1 3.9 2.1 236 238 C 4.9 H 5.0 4.3 4.3 28.0 4.0 4.7 4.3 239 247 H 4.8 H 3.9 1.8 3.4 4.0 3.9 2.4 3.6 248 251 * 1.9 P 24.5 24.2 5.1 21.8 39.5 4.5 3.8 252 285 - 4.5 M 75.0 75.0 62.8 75.0 75.0 75.0 5.8 >>>>>>