Reading input alignment file to find conserved blocks of secondary structure The input structure based alignment from Comparer _____________________________________________ >P1;d1fgha1 C---CCCCCCCCCCCCC-------CCCCCCCCCEEEEEEEEECCCCCCHHHHCCC-----------------------HHHHHHCCCHHHHHHHCCC-------CCCCCCCCC-CCCEECCCCCCEECHHHHHHHHHHCC---CCEEEECCCCC---CCCCCCCHHHHHHHHC------------CEEEEEECCCCHHHHHHHHHCCCEEEEECCHHHHHH--CCCCCEEEEECHHHCCCCCCEEEEEECCC---CCEEEEEEECCC-CHHHHHHHHHCCHHHHHHHHCCC------------------ >P1;d1l5ja2 ------------------------------CCCCCEEEEEEEEEEEEEHHHHCCH-HHHHHCC-----------------------CHHHHHHHCCCC-----CCC----------CCCCCCCCC-CCCHHHHHHHHCCC---CCEEE-EEEEE---EECCCCCHHHHHHHHHHCEEECCEEEEEECCEEEEEEECHHHHHHHHHCCCEEEECCCC------CCCCCCEEEEECC-------CCEEEEC--C---CCCEEEECCCC--CCHHHHHHHHCCHHHHHHHHHHHHHHHHHCCCCCCCCCCCC >P1;d1v7la- ---------------------------------CEEEEEEEECCCCCCHHHHCCC-CCCCC-C-----------------------CHHHHHHHCCCC-----CCC------------------------CHHHHCCC-----CCEEE-CCCCC---CCCCCCCHHHHHHHHH------------CCCEEEECCCCHHHHHHHHHHCCCEEECCCC------CCCCCCEEEEECC-------CCEEEEC--C------EEEECEEC--CHHHHHHHHCCCHHHHHHHCCCCC----------------C >P1;d2b3ya1 CCCCCCCCCCCCCCCCHHHCCCCCCCCCC--CCEEEEEEEEECCCCCCHHHHCCCCCCCCCCHHHHHHHHCCCCHHHCCCCHHHCCCHHHHHHCCCCC-----CCCCCCCCCCCCCEEECCCCCCEEEHHHHHHHHHHCC---CCEEEECCCCC---CCCCCCCHHHHHHHHC------------CEEEEEECCCCHHHHHHHHHCCCEEEEECCCCCHHHHCCCCCCCEEECCCCCCCCCCEEEEEE--CC---C--CEEEEEECCCCHHHHHHHHHCCHHHHHHHHHHC------------------ >P1;d2gp4a1 ---------------------------------------------------------------------------------------------CEEEEEECCEEEEEECCCCCHHHCEEEE-EEEEECCHHHHHHHHHCCCCCCCEEEEECCCCHHHH-CCCCCCCHHHHHHHHHC---------CCCEECCCCCCC---CCCCCCCCEEEECCHHHCCHHHCCCCCCEEEEECC-------CCEEEECCCHHHHHHCCCC----CCCCHHHCCCCHHHCHHHHH-----CCCCHHHCCCCCCCHHHCC >P1;d2hi6a1 ------------------------------------------------------------------------------------------CCCCEECCCCEEEEEEEECCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC------CEEEECCCC---CCCCCCHHHHHHHHH-----------CCCCCEEEECCCCHHHHHHHHHCCCCEEECCCHHHHHH--CCCCCEEEEECC-------CCEEEEEC----------------------------------------------------------- PSA >P1;d1fgha1 a---9158a37664859-------7175156520550000000567010530032-----------------------a825523501320050002-------603023276-4320412546835400700330484a---33000002750---0384615100100020------------202000014028402520041000003026570184--05370300046058044b33040103159---a66450506070-757202104000161375475a7------------------ >P1;d1l5ja2 ------------------------------5168431000010495040530006-7247037-----------------------612500400017-----629----------b08036666-20017206614859---37000-00430---0394615000200021009847a586522420000470286005200220000040707------6072142000203-------6130343--9---47751180a06--57100102739036406873884686367895791a924a9 >P1;d1v7la- ---------------------------------2536230020a55120540004-52382-a-----------------------448401710036-----326------------------------60095087-----20000-02540---0482645000300421------------5010000250282045000210000046809------8074527030304-------602052c--b------54160720--8a6203004030495146459869----------------b >P1;d2b3ya1 7aa6947b931454523137a185a3962--9216401000106661405300029a027b0000510693926295064023037001001200002-----66060400a650230211337542201300430486a---22000001660---0294614000200310------------205000025048400420021000002029c33185190706130104039a08252505040--56---a--440501020169611520408046234414757------------------ >P1;d2gp4a1 ---------------------------------------------------------------------------------------------2664065404403030550777234040-300102426605832774404550000000001201-44306506630150066---------93500000154a---82650030330250033902003057815030108-------7340102179950780939----a061882378745866a606-----72431668341945a858a >P1;d2hi6a1 ------------------------------------------------------------------------------------------6270703169804140110758110672024770306752750564026------400003105---05c080800470465-----------91005000046049301600350700001054770165--084633030407-------70402068----------------------------------------------------------- Translating the sequences *---*************-------***********EEEEEEE******HHHHCC*-----------------------********CHHHHHH*CCC-------CC**CCCCC-**C**CCCCCC**C*HHHHHHHH*CC---CCEEEE*CCCC---CCCCCCCHHHHHHHH*------------C**EEEECCCCHHHHHHHHHCCCEEEE*CC****HH--CCCCCEEEEEC********C*EEEE***C---****EEE***C*-CHHHHHHHHHCCHHHHHHH***C------------------ ------------------------------*****EEEEEEE******HHHHCC*-*******-----------------------CHHHHHH*CCCC-----*CC----------C**CCCCCC-*C*HHHHHHHH*CC---CCEEE-*****---**CCCCCHHHHHHHH**************CCEEEE***CHHHHHHHHHCCCEEEECCC*------CCCCCCEEEEECC-------CCEEEE*--C---****EEE***C--C*HHHHHHHHCCHHHHHHH********************** ---------------------------------**EEEEEEE******HHHHCC*-*****-*-----------------------CHHHHHH*CCCC-----*CC------------------------*HHHH***-----CCEEE-*CCCC---CCCCCCCHHHHHHHH*------------CCCEEEECCCCHHHHHHHHH*CC*EEECCC*------CCCCCCEEEEECC-------CCEEEE*--C------*EEE***C--CHHHHHHHH*CCHHHHHHH***C*----------------* *****************************--****EEEEEEE******HHHHCC********************************CHHHHHH*CCCC-----*CC**CCCCC******CCCCCC****HHHHHHHH*CC---CCEEEE*CCCC---CCCCCCCHHHHHHHH*------------C**EEEECCCCHHHHHHHHHCCCEEEE*CC****HH*CCCCCC*EEE*CC*********EEEE--*C---*--*EEE***C**CHHHHHHHHHCCHHHHHHH***C------------------ ---------------------------------------------------------------------------------------------***************CCCCC***C****-*****C*HHHHHHHH*CC***CCEEEE*CCCC****-CCCCC**HHHHHH****---------CCCEE**CCCC*---*****CCCEEEECC*****HH*CCCCCCEEEEECC-------CCEEEE*************----C**CHHH****HH*CHHHHH-----C****************** ------------------------------------------------------------------------------------------******CC**********CCCCC***C**CCCCCC**C**********C------*EEE*CCCC---CCCCCC*HHHHHHHH-----------**CCCEEEECCCCHHHHHHHHHCCC*EEECCC****HH--CCCCCEEEEECC-------CCEEEE**----------------------------------------------------------- 52016.tem _________________________________ -------------------------------****EEEEEEE******HHHHCC*-*****-*-----------------------CHHHHHH*CCCC-----*CC**CCCCC***C**CCCCCC**C*HHHHHHHH*CC---CCEEEE*CCCC---CCCCCCCHHHHHHHH*------------CCCEEEECCCCHHHHHHHHHCCCEEEECCC****HH-CCCCCCEEEEECC-------CCEEEE***C---****EEE***C*-CHHHHHHHHHCCHHHHHHH***C*----------------* Structural block scores 0 30 - 4.2 M 28.2 72.7 75.0 10.2 75.0 75.0 31 34 * 3.0 P 3.0 4.8 39.2 4.5 75.0 75.0 35 41 E 4.3 M 0.7 0.7 2.3 0.9 75.0 75.0 42 47 * 2.7 P 3.2 3.7 3.9 3.8 75.0 75.0 48 51 H 4.3 M 2.0 2.0 2.2 2.0 75.0 75.0 52 53 C 4.3 M 1.5 0.0 0.0 0.0 75.0 75.0 56 60 * 3.4 M 75.0 4.0 4.0 6.2 75.0 75.0 63 85 - 4.4 M 50.7 75.0 75.0 3.6 75.0 75.0 87 92 H 4.2 M 1.8 2.0 4.0 0.7 75.0 40.0 94 97 C 4.2 M 19.2 2.0 2.2 0.5 4.0 2.8 98 102 - 4.1 M 75.0 75.0 75.0 75.0 3.8 5.4 104 105 C 4.1 M 3.0 5.5 4.0 3.0 1.5 2.0 106 107 * 2.7 P 1.5 75.0 75.0 3.0 1.5 1.0 108 112 C 4.3 M 4.0 75.0 75.0 4.1 3.4 4.2 113 115 * 2.9 P 27.3 75.0 75.0 2.3 5.3 2.3 117 118 * 1.9 P 2.0 4.0 75.0 1.0 2.0 1.0 119 124 C 4.2 M 4.3 4.5 75.0 3.3 13.7 3.8 125 126 * 2.3 P 4.0 38.5 75.0 3.0 0.5 3.0 129 136 H 4.3 M 2.1 3.4 12.9 1.9 4.0 3.6 138 139 C 4.4 M 7.2 7.0 75.0 8.2 5.5 40.5 140 142 - 4.5 M 75.0 75.0 75.0 75.0 2.7 75.0 143 144 C 4.5 M 3.0 5.0 1.0 2.0 5.0 75.0 145 148 E 4.7 H 0.0 18.8 18.8 0.0 0.0 1.0 150 153 C 4.5 M 3.5 1.8 2.8 3.2 0.0 2.2 154 156 - 4.5 M 75.0 75.0 75.0 75.0 1.0 75.0 157 163 C 4.7 H 3.9 4.0 4.1 3.7 13.3 4.8 164 171 H 4.9 H 0.5 0.5 1.1 0.8 3.2 3.2 173 184 - 4.3 M 75.0 5.4 75.0 75.0 57.2 63.3 185 187 C 4.2 M 1.3 2.7 2.0 2.3 5.7 1.7 188 191 E 4.8 H 0.0 0.0 0.0 0.0 0.0 0.0 192 195 C 4.6 H 1.8 3.2 2.2 2.8 2.5 3.5 196 204 H 4.5 M 2.8 2.6 2.3 2.2 28.5 3.0 205 207 C 4.8 H 0.3 0.7 0.3 0.3 1.0 2.3 208 211 E 4.8 H 0.8 1.0 1.0 0.5 2.0 0.2 212 214 C 4.5 M 2.7 2.3 4.7 3.7 1.7 3.0 215 218 * 2.3 P 3.2 58.0 58.5 4.9 3.8 3.8 219 220 H 4.3 M 6.0 75.0 75.0 6.5 1.0 5.5 222 227 C 4.9 H 15.0 3.3 4.3 3.8 4.0 16.0 228 232 E 4.8 H 1.4 0.8 2.6 1.6 1.8 2.0 233 234 C 4.8 H 3.0 1.5 2.0 1.5 4.0 3.5 235 241 - 4.1 M 5.1 75.0 75.0 5.2 75.0 75.0 242 243 C 4.3 M 1.5 3.5 3.0 2.5 5.0 3.5 244 247 E 5.0 H 1.2 2.5 2.2 2.2 1.2 1.5 248 250 * 2.9 P 3.0 51.0 54.2 51.7 3.3 29.7 252 254 - 4.5 M 75.0 75.0 75.0 75.0 4.7 75.0 255 258 * 2.9 P 6.6 5.8 57.5 41.1 6.0 75.0 259 261 E 4.2 M 3.3 3.3 3.7 3.0 29.0 75.0 262 264 * 2.7 P 2.0 3.5 3.0 0.3 75.0 75.0 269 277 H 4.3 M 2.3 2.3 2.8 3.1 5.8 75.0 278 279 C 4.3 M 0.0 4.5 1.5 4.0 7.0 75.0 280 286 H 4.4 M 3.9 4.9 4.7 3.4 25.5 75.0 287 289 * 2.7 P 7.5 6.3 7.3 5.3 75.0 75.0 292 307 - 4.1 M 75.0 6.6 75.0 75.0 5.3 75.0 >>>>>>