Reading input alignment file to find conserved blocks of secondary structure The input structure based alignment from Comparer _____________________________________________ >P1;d2idra- ---------------CCEEEEEEEEEEECCCCCEEE-------C--C--EEECCEEEEEEHH----HHHHHHCCCCCHHHCC-----------CCCEEEEEEHHHCCCCCCC-CCC-------------------------CCEEEEEEEC---CCCCHHHHHHHHHHHHCCCCC---CHHHEEEEEEEECC----CEEEEEEECCCCCHHHHHHHHHHHC-CCCC-C--CCEEEEHHHHHCC----------CCCEEC---------------- >P1;d2jgba- CCCCCCC-------CCCEEEEEEEEEEEEECCCCCC-------CHHHHHHHEEEEEEEEEHH----HHHHHHCCCCCHHHCC-----------CEEEEEEEECCCCCCCCCC-CCC-------------------------CCEEEEEEEC---CCCHHHHHHHHHHHHHCCCC---CCCCCEEEEEEEECC---CCEEEEEEECCCCCHHHHHHHHHHHHHHCCCCCCCCEEEEEHHHHHHCCC------CC--CCCC---------------- >P1;d2q4ka- ------------------------------------CCCCCHHHHHHHCCCCCCCEEEECCCCCCCCHHHHHHHC-CCCCCCCCCCCCCCCCCCCCCEEEECCCCCCCCCCHHHHHHHHHHHHCCCCCCCHHHHHHHHHCCCCCCEEEECCCCC-HHHHHHHHHHHHHHCCC---------CCCEEEECCCCCCCCCCCEEEEECCCCCHHHHHHHHHHHHHC-CCC--CCEEEEEHHHHHCCCCCCCCCCCCCCCEEEEECCEEEEECCCCEEC >P1;d3hxia1 ---------------CCEEEEEEEEEEECC--CCCC-------HHHH----EEEEEEEEEHH----HHHHHHHCCCCCC--C-----------CCCEEEEEECCCCCCCCCH-HHH-------------------------CCEEEEEECC--CCCCHHHHHHHHHHHHHCCCCCCHHHHHHEEEEEEECCC----CCEEEEEECCCCCHHHHHHHHHHHHHHHCCCC--CEEEEEHHHHHHCCC------CCCCCEEE---------------- >P1;d4ue8a1 ---------------CCEEEEEEEEEEECC-------------------CCCEEEEEEEEHH----HHHHHHHHCCCHHHCC-----------CCCEEEEEECCCCCCCCCC-CCC-------------------------CCEEEEEEEECCCHHHHHHHHHHHHHHHHCCCC---CCHHHEEEEEEEEEC---CEEEEEEEECCCCCHHHHHHHHHHHHHHHCCCHHHCCEEEEHHHC----------------------------------- >P1;d6fc0a1 ----CCCCCCCCCCCCCEEEEEEEEEEECCCCCC----------CCCCCCCEEEEEEEEEHH----HHHHHHCCCCCHHHCC-----------CCEEEEEEECCCCCCCCCC-CCC-------------------------CCEEEEEEECCCCCCCHHHHHHHHHHHHHCCCC-CCCCCCCEEEEEEEECC---CCEEEEEEECCCC-CHHHHHHHHHHHHHCCCCCCCCCEEEECCHHHHH---------C--CCCC---------------- PSA >P1;d2idra- ---------------5870713010203549c6784-------b--c--5342664405245----604921781740370a-----------3501010004718299657-214-------------------------7002010418---347039103400300062507---42a10000001049----60400020240a5680023006302-20a2-9--6000512538878----------a54151---------------- >P1;d2jgba- ba3834a-------a276062200002051729493-------8396349307623100045----2048316816504718-----------7100000004b15004528-205-------------------------8002100407---4b302900340040008360---50b710000001015---82010000044194a90144043006620a129b190513307615869b------98--6872---------------- >P1;d2q4ka- ------------------------------------aa385995679689b336422020863657605810872-10160125039c020963002000208a48874072a605630873395c6616494048005528022010370426-83035004500400065---------502000020366a2a504000217402557502700710072-905--340302020064060999095a032200205469250214399661 >P1;d3hxia1 ---------------777073300001137--5c38-------5450----05523405245----6045108724400--a-----------6620000012a06023507-505-------------------------9001000504--b82724400220040007260769401600000001038----a1200000123857a10230061016308087--30100008604859a------b4804142---------------- >P1;d4ue8a1 ---------------57707350001223a-------------------a605545205144----3036118826300508-----------6500000014c2402463a-404-------------------------900210030671769702810250031008250---821820000002045---830300000340b588016200540474090aad2515132066b----------------------------------- >P1;d6fc0a1 ----3388588a3c774706440000223352c8----------a737a7214535105041----5038118924304706-----------5600000024a05025518-605-------------------------800201160a62971903300230030007370-18990700000001027---a302000105327-3740270053017105058a330604003a9268---------b--9240---------------- Translating the sequences ---------------CCEEEEEEEEEEECC**C***-------*--*--**E**EEEEEEHH----HHHHHH*CCCCHHHCC-----------CCCEEEEEE***CCCCCCC-CCC-------------------------CCEEEEEEEC---CCC*HHHHHHHHHHHHCCCC*---C***EEEEEEEECC----CEEEEEEECCCCCHHHHHHHHHHH*-**CC-C--C*EEEEHHHHH*C----------**C***---------------- *******-------*CCEEEEEEEEEEE****C***-------********EEEEEEEEEHH----HHHHHH*CCCCHHHCC-----------C**EEEEEECCCCCCCCCC-CCC-------------------------CCEEEEEEEC---CCCHHHHHHHHHHHHHCCCC---*C***EEEEEEEECC---CCEEEEEEECCCCCHHHHHHHHHHHHHH*CCCC**C*EEEEHHHHH*C**------*C--C***---------------- ------------------------------------*******************EEEE********HHHHH**C-C***CC***********CCC*EEEE*CCCCCCCCC******************************CC**EEEE*C**C-**HHHHHHHHHHHH*CC---------***EEEE**CC***CC**EEEEECCCCCHHHHHHHHHHHHH*-CCC--*C*EEEEHHHHH*C*********C**C******************* ---------------CCEEEEEEEEEEECC--C***-------****----EEEEEEEEEHH----HHHHHH*CCCC**--C-----------CCCEEEEEECCCCCCCCC*-***-------------------------CCEEEEEE*C--CCCCHHHHHHHHHHHHHCCCC********EEEEEEE*CC----C*EEEEEECCCCCHHHHHHHHHHHHHH*CCCC--C*EEEEHHHHH*C**------*C**C***---------------- ---------------CCEEEEEEEEEEECC-------------------***EEEEEEEEHH----HHHHHH**CCCHHHCC-----------CCCEEEEEECCCCCCCCCC-CCC-------------------------CCEEEEEEE***C***HHHHHHHHHHHHHCCCC---*C***EEEEEEEE*C---C*EEEEEEECCCCCHHHHHHHHHHHHHH*CCC***C*EEEEHHH*----------------------------------- ----***********CCEEEEEEEEEEECC**C*----------*******EEEEEEEEEHH----HHHHHH*CCCCHHHCC-----------CC*EEEEEECCCCCCCCCC-CCC-------------------------CCEEEEEEEC**CCCCHHHHHHHHHHHHHCCCC-***C***EEEEEEEECC---CCEEEEEEECCCC-*HHHHHHHHHHHHH*CCCC**C*EEEE**HHH**---------C--C***---------------- 55418.tem _________________________________ ---------------CCEEEEEEEEEEECC**C***-------********EEEEEEEEEHH----HHHHHH*CCCCHHHCC-----------CCCEEEEEECCCCCCCCCC-CCC-------------------------CCEEEEEEEC**CCCCHHHHHHHHHHHHHCCCC---*C***EEEEEEEECC---CCEEEEEEECCCCCHHHHHHHHHHHHHH*CCCC**C*EEEEHHHHH*C**------*C**C***---------------- Structural block scores 0 14 - 4.4 M 75.0 39.1 75.0 75.0 75.0 25.1 15 16 C 4.5 M 6.5 4.5 75.0 7.0 6.0 5.5 17 27 E 4.5 M 2.2 1.6 75.0 2.0 2.5 2.3 28 29 C 4.2 M 4.5 3.0 75.0 5.0 6.8 3.0 30 31 * 3.4 M 10.8 4.5 75.0 75.0 75.0 3.5 33 35 * 3.2 M 6.3 5.3 75.0 7.8 75.0 52.7 36 42 - 4.5 M 75.0 75.0 7.9 75.0 75.0 75.0 43 50 * 2.6 P 41.5 5.6 7.7 39.2 58.3 15.2 51 59 E 4.6 H 3.7 2.1 2.4 2.9 3.0 2.7 60 61 H 4.5 M 4.5 4.5 7.0 4.5 4.0 2.5 62 65 - 4.5 M 75.0 75.0 5.2 75.0 75.0 75.0 66 71 H 4.9 H 3.7 3.0 3.3 2.7 2.3 3.0 73 76 C 4.7 H 5.0 5.0 21.2 4.2 4.8 4.5 77 79 H 4.1 M 3.3 3.7 2.3 25.0 1.7 3.7 80 81 C 4.8 H 5.2 4.5 0.5 42.8 4.0 3.0 82 92 - 4.5 M 75.0 75.0 4.4 75.0 75.0 75.0 93 95 C 4.5 M 2.7 2.7 1.0 4.7 3.7 3.7 96 101 E 4.8 H 0.3 0.0 0.7 0.2 0.2 0.3 102 111 C 4.8 H 5.8 4.0 5.8 3.5 4.8 4.0 113 115 C 4.1 M 2.3 2.3 3.7 3.3 2.7 3.7 116 140 - 4.5 M 75.0 75.0 4.7 75.0 75.0 75.0 141 142 C 5.0 H 3.5 4.0 4.0 4.5 4.5 4.0 143 149 E 4.7 H 1.1 1.0 2.1 0.9 0.9 1.4 151 152 * 3.4 M 75.0 75.0 3.0 75.0 4.0 4.0 153 156 C 4.2 M 22.2 23.4 23.0 7.1 7.2 6.5 157 169 H 4.9 H 1.8 1.7 1.6 1.4 1.7 1.1 170 173 C 4.8 H 3.2 4.2 40.2 3.8 3.8 4.2 174 176 - 4.1 M 52.3 75.0 75.0 7.3 75.0 28.0 179 181 * 1.6 P 4.5 6.5 51.7 2.3 3.7 2.3 182 189 E 4.7 H 0.1 0.1 0.5 0.1 0.2 0.1 190 191 C 4.8 H 6.5 3.0 4.5 5.5 4.5 4.5 192 194 - 4.5 M 75.0 75.0 6.2 75.0 75.0 75.0 195 196 C 4.4 M 40.5 5.0 7.8 42.8 5.5 6.8 197 203 E 4.8 H 0.9 0.1 1.0 0.4 0.4 0.4 204 208 C 4.9 H 4.3 4.4 3.6 3.8 4.7 18.4 209 222 H 4.8 H 7.6 3.5 3.1 2.9 3.5 2.9 224 227 C 4.7 H 24.1 5.6 22.2 5.8 7.5 4.5 228 229 * 3.0 P 75.0 6.2 39.0 75.0 7.8 6.8 232 235 E 5.0 H 1.5 3.0 1.2 0.2 2.8 2.5 236 240 H 4.6 H 5.2 3.8 2.4 3.6 19.7 4.9 243 244 * 3.4 M 75.0 10.2 4.5 9.8 75.0 75.0 245 250 - 4.5 M 75.0 75.0 7.1 75.0 75.0 75.0 253 254 * 3.4 M 7.8 75.0 2.0 4.0 75.0 75.0 256 258 * 1.9 P 2.3 5.7 0.7 2.3 75.0 2.0 259 274 - 4.5 M 75.0 75.0 4.5 75.0 75.0 75.0 >>>>>>