Reading input alignment file to find conserved blocks of secondary structure The input structure based alignment from Comparer _____________________________________________ >P1;d1gl4a1 -------CCEEEEEEEEEEEEEECCCCCCEEEEEEEEEEEEECCCCEEEEEEE-CCCHHHHHHHCCCCHHHHHHHHHCCEECCCCC----CHHHHHC---CEEEEEEEEEECCCCCCEEEEEEEECCCCCCCEECEEEEEEEECCCCC-------CCEEECCCEEEEEEEE--CCEEEEEEEEEEEEECCCCCCCCCCEEEEEEEEEEEECCCCCCCCCCCCCC----CEEEEEEEEEEEEEECC---CCEEEEEEEEEEECCC------- >P1;d2c9ja- ---------CEEEEEEEEEEECC------EEEE-EEEEEEEECCCCEEEEEEEECCCCCCCCCHHHCCCCC---CCCCCCCCCCCC----CCCHHHCC--CCEEEEEEEEECCC-CEEEEEEEEEEE--CCEEEEEEEEEEE--CCCCCCCCCCCCEE-EECCEEEEEEEEC--CEEEEEEEEEEEECC--------CCEEEEEEEEEEEECCC----CCCCCC-----CEEEEEE-EEEEEE--CHHHCEEEEEEEEEEECC-----CCC >P1;d2g6ya- ---------CEEEEEEEEEEECC------EEEE-EEEEEEEEHHHCEEEEEEEECCC-CCCCCHHHHCCCC---CHHHCCCCCC----CCCHHHHHHHC-CCEEEEEEEEECCC-CEEEEEEEEEEE--CCEEEEEEEEEEE--CCCCCCHHHCCCEE-EECCEEEEEEECCC-CEEEEEEEEEEEECC--------CCEEEEEEEEEEEECC-----CCCHHHHCCCCCEEEEEE-EEECCC-----CCEEEEEEEEEEECCC------- >P1;d3gb3a- CCCCCHHHCCEEEEEEEEEEECC------EEEE-EEEEEEECCCCCEEEEEEEECCC-CCCCCCHHHCCCC---CHHHCCCCCCCC----CHHHHCCC--CCEEEEEEEEECCC-CEEEEEEEEEEE--CCEEEEEEEEEEE--CCCCCCCCCCCCEE-EECCEEEEEEECCC-CEEEEEEEEEEEECC--------CCEEEEEEEEEEEECCC---CCCCCCC-----CEEEEEE-EEEECCCCCCC-CEEEEEEEEEEECCCCCCCCCC >P1;d4q9wa1 ----CCCCCCEEEEEEEEEEECC------EEEE-EEEEEEEECCCCEEEEEEEEEECCCCCCCCHHHHCCC---CCCCCCCCCCCC----CHHHHCCC--CCEEEEEEEEECCC-CEEEEEEEEEEE--CCEEEEEEEEEEE--CCCCCCCCCCCCEE-EECCEEEEEEEEC--CEEEEEEEEEEEECC--------CCEEEEEEEEEEEECC-----CCCCCC-----CEEEEEE-EEEEEE--CCCCCEEEEEEEEEEEEC-------- >P1;d6l27a- -CCHHHHCCCEEEEEEEEEEECC------EEEE-EEEEEEEEHHHCEEEEEEEECCC-CCCCCHHHHCCCC---CHHHCCCCHHHHHH--CHHHHCCC--CCEEEEEEEEECCC-CEEEEEEEEEEE--CCEEEEEEEEEEE--CCCCCCCCCCCCCCCCCCCEEEEEEECCCCCCEEEEEEEEEECCC--------CCEEEEEEEEEEEECCC---CCCCCCC-----CEEEEEE-EEEECCCCCCC-CEEEEEEEEEEECCCC------ >P1;d6m9za- -------CCCCEEEEEEEEEECC------EEEE-EEEEEEEECCCCEEEEEEEECCC-CCCCCHHHHHHHCCCCCHHHCEEC-C----EECHHHHHHHCCCCEEEEEEEEECCC-CEEEEEEEEEEE--CCEEEEEEEEEEE--CCCCCCCCCCCCEE-EECCEEEEEEEEEC-CEEEEEEEEEEEECC--------CCEEEEEEEEEEEECC-----CCCHHHHCC-CCEEEEEE-EEEEEEE----CCEEEEEEEEEEECCC------- PSA >P1;d1gl4a1 -------86535034505050214a5891240690605050227702050204-70225001000000000100000003347b15----0034006---070206030305b47940506050715496730307050642017046-------7070507515040528--a3405062416020622b8ba46944545030303040a17997ca49913----92010505508060558---8510502020300248------- >P1;d2c9ja- ---------9160302040402a------5704-040850451830506050705ba95030000000100---00000604bb07----20027015--5004060504033a-020705040438--9930304060605--90289210053404-5023160303279--910005060402168--------8650607010505023b----b1810b-----6020515-041564--584142030115020366-----a89 >P1;d2g6ya- ---------32605040323049------6602-056146031a704030807044a-6060001000100---00001303bc----260003501a4-5006030406053a-030404060614--b820204060606--a03aa020249503-502314040425b7-34030506030015a--------a760406060706075-----501520181c73030314-160a07-----4550002020402577------- >P1;d3gb3a- 59036407460604040802037------6704-0105360755003070301054b-8010012000100---01000404cb12----00001006--400105040504b0-030605040708--9430206050506--c0579220066406-50452504043598-500303070003159--------8851203040403042b---3a05108-----5020124-080774b8196-20030523040356899b5aa8 >P1;d4q9wa1 ----a506760406050504039------6701-0507071505603030504047546020000000100---00000604b803----20014005--50030603050539-020606040408--9410406040604--8038a220053505-402513040226b--82030106020426b--------a950405070407044-----b0730a-----5020416-051475--593246010313040571-------- >P1;d6l27a- -4056408951504040802038------5701-02074502066040502010477-9000000000100---01000402940560--00000005--70010401050690-010505030206--ca20107080506--7069933003540336066250504209a4500407040504167--------9650102060104032a---7704406-----a020507-0606427c196-50020403040341ab------ >P1;d6m9za- -------6407504030312039------7904-053826151950405070704b7-607000100000000000000203-9----84000041025522060606050439-050404040806--9220306050405--b0389220148205-60261404030475-420203160203065--------b750306050406066-----407770285-34030404-07062a6----33501030406021a8------- Translating the sequences -------*C*EEEEEEEEEEE********EEEE*EEEEEEEECCCCEEEEEEE-CCC******H***C*******HH*C**CCC**----CHHHH*C---C*EEEEEEEEECCC*C*EEEEEEEE****CC*EE*EEEEEEE**CCCC-------C*E*E*CCEEEEEEE*--*CEEEEEEEEEEEE*C********C*EEEEEEEEEEE*CC*****CCCCCC----**EEEEEE*EEEE****---*CEEEEEEEEEEECCC------- ---------CEEEEEEEEEEECC------EEEE-EEEEEEEECCCCEEEEEEEECCC*CCCCCHHH*CCCC---C***CCCCCC**----C**HH*C*--CCEEEEEEEEECCC-CEEEEEEEEEEE--CCEEEEEEEEEEE--CCCCCCCCCCCCEE-EECCEEEEEEE*C--CEEEEEEEEEEEECC--------CCEEEEEEEEEEEECC*----CCCCCC-----CEEEEEE-EEEE**--****CEEEEEEEEEEECC-----*** ---------CEEEEEEEEEEECC------EEEE-EEEEEEEE***CEEEEEEEECCC-CCCCCHHHHCCCC---CHH*CCCCCC----**CHHHH****-CCEEEEEEEEECCC-CEEEEEEEEEEE--CCEEEEEEEEEEE--CCCCCC***CCCEE-EECCEEEEEEE*C*-CEEEEEEEEEEEECC--------CCEEEEEEEEEEEECC-----CCC********CEEEEEE-EEE***-----*CEEEEEEEEEEECCC------- ********CCEEEEEEEEEEECC------EEEE-EEEEEEE*CCCCEEEEEEEECCC-CCCCC*HHHCCCC---CHH*CCCCCC**----CHHHH*C*--CCEEEEEEEEECCC-CEEEEEEEEEEE--CCEEEEEEEEEEE--CCCCCCCCCCCCEE-EECCEEEEEEE*C*-CEEEEEEEEEEEECC--------CCEEEEEEEEEEEECC*---*CCCCCC-----CEEEEEE-EEEE*******-CEEEEEEEEEEECCC******* ----****CCEEEEEEEEEEECC------EEEE-EEEEEEEECCCCEEEEEEEE**C*CCCCC*HHH*CCC---C***CCCCCC**----CHHHH*C*--CCEEEEEEEEECCC-CEEEEEEEEEEE--CCEEEEEEEEEEE--CCCCCCCCCCCCEE-EECCEEEEEEE*C--CEEEEEEEEEEEECC--------CCEEEEEEEEEEEECC-----CCCCCC-----CEEEEEE-EEEE**--****CEEEEEEEEEEE*C-------- -*******CCEEEEEEEEEEECC------EEEE-EEEEEEEE***CEEEEEEEECCC-CCCCCHHHHCCCC---CHH*CCCC******--CHHHH*C*--CCEEEEEEEEECCC-CEEEEEEEEEEE--CCEEEEEEEEEEE--CCCCCCCCCCCC*****CCEEEEEEE*C**C*EEEEEEEEEE*CC--------CCEEEEEEEEEEEECC*---*CCCCCC-----CEEEEEE-EEEE*******-CEEEEEEEEEEECCC*------ -------*CC*EEEEEEEEEECC------EEEE-EEEEEEEECCCCEEEEEEEECCC-CCCCCHHHH***C***CHH*C**C-C----**CHHHH*****CCEEEEEEEEECCC-CEEEEEEEEEEE--CCEEEEEEEEEEE--CCCCCCCCCCCCEE-EECCEEEEEEE***-CEEEEEEEEEEEECC--------CCEEEEEEEEEEEECC-----CCC******-*CEEEEEE-EEEE***----*CEEEEEEEEEEECCC------- 54511.tem _________________________________ ----****CCEEEEEEEEEEECC------EEEE-EEEEEEEECCCCEEEEEEEECCC*CCCCCHHHHCCCC---CHH*CCCCCC**----CHHHH*C*--CCEEEEEEEEECCC-CEEEEEEEEEEE--CCEEEEEEEEEEE--CCCCCCCCCCCCEE-EECCEEEEEEE*C*-CEEEEEEEEEEEECC--------CCEEEEEEEEEEEECC*---*CCCCCC----*CEEEEEE-EEEE********CEEEEEEEEEEECCC------- Structural block scores 0 3 - 4.3 M 75.0 75.0 75.0 4.2 75.0 21.0 75.0 4 7 * 3.4 M 58.2 75.0 75.0 4.2 5.4 4.5 57.8 8 9 C 4.5 M 5.5 42.0 39.0 5.0 6.5 7.0 2.0 10 20 E 5.0 H 2.7 1.8 2.3 2.2 2.2 2.2 2.3 21 22 C 4.6 H 1.5 6.2 6.5 5.0 6.0 5.5 6.0 23 28 - 4.6 H 6.2 75.0 75.0 75.0 75.0 75.0 75.0 29 32 E 5.0 H 3.0 4.0 3.5 4.2 3.5 3.2 5.0 34 41 E 5.0 H 2.2 3.2 3.1 2.8 3.1 2.5 3.8 42 45 C 4.4 M 4.0 3.0 4.6 2.5 2.8 3.0 3.8 46 53 E 5.0 H 11.0 2.9 2.8 1.8 1.9 1.5 2.9 54 56 C 4.7 H 3.0 9.0 6.2 6.8 5.3 6.0 7.5 58 62 C 4.6 H 1.2 1.6 2.4 1.8 1.6 1.8 2.6 63 66 H 4.4 M 0.0 0.0 0.2 0.8 0.0 0.0 0.2 67 70 C 4.3 M 0.0 0.2 0.2 0.2 0.2 0.2 0.0 71 73 - 4.2 M 0.3 75.0 75.0 75.0 75.0 75.0 0.0 75 76 H 4.2 M 0.0 0.0 0.0 0.5 0.0 0.5 0.0 78 83 C 4.5 M 4.8 5.5 5.2 5.3 4.9 3.2 14.8 84 85 * 2.5 P 3.0 3.5 75.0 1.5 1.5 2.5 75.0 86 89 - 4.4 M 75.0 75.0 39.5 75.0 75.0 39.0 40.5 91 94 H 4.8 H 1.8 2.2 2.0 0.2 1.2 0.0 1.0 98 99 - 4.4 M 75.0 75.0 39.5 75.0 75.0 75.0 5.0 100 101 C 4.8 H 3.5 2.5 2.5 2.0 2.5 3.5 2.0 102 110 E 5.0 H 1.6 2.1 2.1 1.7 1.9 1.2 2.6 111 113 C 5.0 H 6.8 5.5 6.2 5.2 5.7 5.0 5.3 116 126 E 4.9 H 3.0 3.0 2.5 3.0 2.7 2.0 2.8 127 128 - 4.6 H 6.5 75.0 75.0 75.0 75.0 75.0 75.0 129 130 C 5.0 H 6.5 9.0 9.8 6.5 6.5 11.5 5.5 131 141 E 4.9 H 2.7 2.5 2.4 2.5 2.3 2.6 2.3 142 143 - 4.6 H 0.5 75.0 75.0 75.0 75.0 75.0 75.0 144 155 C 4.7 H 45.8 3.6 4.7 4.5 3.9 4.1 4.2 156 157 E 4.4 M 3.5 2.0 1.5 3.0 2.5 1.5 2.5 159 160 E 4.4 M 2.5 2.5 2.5 2.5 2.0 3.0 3.0 161 162 C 5.0 H 6.0 2.5 2.5 4.5 3.5 6.0 4.0 163 169 E 5.0 H 2.4 2.1 2.1 2.6 1.7 2.6 1.7 175 186 E 4.9 H 2.5 1.6 1.8 1.4 1.7 2.1 1.6 187 188 C 4.8 H 4.0 7.0 7.8 7.0 8.8 6.5 5.5 189 196 - 4.6 H 7.8 75.0 75.0 75.0 75.0 75.0 75.0 197 198 C 4.8 H 4.0 7.0 8.8 8.0 9.8 7.5 9.2 199 210 E 5.0 H 2.2 2.4 2.9 1.8 2.7 1.6 2.4 211 212 C 5.0 H 5.8 2.5 6.0 3.0 4.0 2.5 6.0 214 216 - 4.6 H 8.3 75.0 75.0 75.0 75.0 75.0 75.0 218 223 C 4.6 H 6.1 5.5 2.2 4.1 5.3 3.5 4.2 224 227 - 4.3 M 75.0 75.0 5.6 75.0 75.0 75.0 22.5 230 235 E 5.0 H 1.8 2.2 1.8 1.5 2.2 2.3 1.8 237 240 E 4.9 H 3.5 2.5 4.4 3.8 2.5 3.0 3.2 241 248 * 2.6 P 31.4 22.2 48.2 15.2 22.6 14.6 40.2 250 260 E 5.0 H 1.2 1.5 1.4 1.8 2.1 1.5 1.9 261 263 C 4.7 H 4.7 29.0 6.3 6.3 27.7 5.2 6.5 264 270 - 4.4 M 75.0 46.8 75.0 9.1 75.0 65.9 75.0 >>>>>>