Reading input alignment file to find conserved blocks of secondary structure The input structure based alignment from Comparer _____________________________________________ >P1;d1xfja- -------CCCEECCHHHHCCCCEEEEEECCCCCCCCHHHCCCCCCCCCCCCHHHHHHHHHHHHHHCCCCHHHEEECCCCCCC------CCEECC----------CCCCC--------CCC------CCCEEEECC---------------------CCCEEEE-C-CCCEEEEEEECC----CCEEEEEEEC-----------HHHHHHCHHHHHHHCC--CCCCCHHHCEEEECCCCCCCC-CEEEHHHHHHHHHHCC-CHHHHEEECCCCCEEEECHHHHHHHHHHHCCCC---EEEECCCCCC------------CCCCCCCCHHHHHHCCCCCCCCCCEEEEEC------------------------------ >P1;d1z9ta- --------CCEECCC---CCCCEEEEEECCCCCCCCCCCCCCCCCCCCCCCHHHHHHHC-CHHHHCCCC--CCCCCCCCCC-------CEEECC----------CCC-----------CC------CCCEEEECC---------------------CCCEEEE-C-CCCEEEEEEECC----CCCEEEEEEC-----------HHHHHHCHHHHHHHCC----CCCHHHEEEEECCCCCC-C-CEECC--CCCC-CCC-HHHHHHEEEE--CCEEEECHHHHHHHHHHHCCCC---EEEECCCCCC------------CCCCCCCCCCCC------CCCC-CEEEEEC------------------------------ >P1;d2f9zc1 ---------------------------------------------------------------------------------------------------------------------CEEECC---CCCEEEEEC---------------------CCEEEEEEE-CCCEEEEEEECC----CCEEEEEEECCCCCC-CCCCCHHHCHHHHHHHHHHHHHC-CCCCHHHCEEEEEECCCCC--------------------------CCC-----CCCHHHHHHHHHHHHHHHCCCCEEEEEECCC------------CCEEEEEECC------CCEEEEECCCCEEEE----------------------------- >P1;d6t0ya- CCCEEECCCCEEEECC-HHHCCCEEEEECCCCCCCCHHHCCCCCCCCCCCCHHHHHHHHHHHHHHHCCCHHHEECCCCCCCC------CEEECC----------HHHCCCCCCCHHHCCC------CCCEEEECC---------------------CCCEEEEEE-CCCEEEEEEECC----CCEEEEEEEC-----------HHHHHCCHHHHHHHHHHHCCCCCHHHCEEEECCCCCCCC-CEECHHHHHHHHHHCCCCCCCCEEE-EECCEEEECHHHHHHHHHHHCCCCHHH-EEECCCCCC------------CCCCCCCCCCCCC----CCCCCEEEEEECCC----------------------------- >P1;d6yhma1 -------------------------------------------------CHHHHHHHHHHHHHCCCHHHHCCCCCCCCCCCCCCCCCCEEEEEECCCCCCCEEECCCCCCCCCCHHHEECCCCCCCEECEEEEEECCCCCCCCCCCCHHHHCCCEEEEEEEEECCCCEEEEEEEEEHHHCCCCCCEEEECCCCCCCEEEEEEEC------------------------CEEEEEEEEECCCCCCCCCCHHHHHHHHHHHHHHCCCCCCCCC-----CCCHHHHHHHHHHHCC----EEEEEEECCCCCHHHCCCCCCCCEEEEEEECCCCCC----CCEEEEEEEEEEECCEEEEEEEEEEEEECCCEEEEEEEEEEC PSA >P1;d1xfja- -------b1301407305818403000001460309c416100021708078930540044007107465740010624433------503208----------73279--------733------600000053---------------------6900000-1-012000000039----3400000000-----------2500054005300634--718064640000000000270-1302380064047617-a0261059077a842302003002220360707---7332043103------------236730005210857a3c130200000005------------------------------ >P1;d1z9ta- --------8312600---5217020000014603086414200033a1a0688308502-403941a03--8023062347-------801508----------a2b-----------74------600000075---------------------6420000-1-013000000047----0700000000-----------2600171002601710----92747300000000004-2-12146--1450-951-b506800777--cb51303004003000343707---4032083104------------746a20007414------7003-0000007------------------------------ >P1;d2f9zc1 ---------------------------------------------------------------------------------------------------------------------555605---705310272---------------------5010006a0-221000001037----160000000433619-c6a36302102200620043046-4705383020000000349--------------------------a5a-----9845065018104610863a08143302888------------3402010306------505020316874542----------------------------- >P1;d6t0ya- 9220643971004050-7109b00000001680408a51520000031b065720160043008108040630000304562------705304----------4912440036487007------610000043---------------------200000000-002000000039----3300000001-----------150017400330060054618151750200000001352-12055600640462049b1740085-569451103003002100242703991-022091000------------536a200064239----36001000000253----------------------------- >P1;d6yhma1 -------------------------------------------------a587404501630260506004320000045054020401000004647ab13515a30559943920108845bb000000001027004a10760720561203860000102101200000102065056940000000002510000024a------------------------640000000114a3a701134002100200030083a62b15a-----8220210040005206----3000001026a5741409493a20220100459146----8000000000013c9803020000001668725257332251 Translating the sequences -------*CCEE********CC*EEEEECCCCCCCC***CCCCCCCCCCCCHHHHHHHHHHHHHHCCCCH*****CCCCCCC------C*EECC----------CCCCC--------CCC------CCCEEEECC---------------------CCCEEEE-C-CCCEEEEEEECC----CCEEEEEEEC-----------HHHHHHCHHHHHHH**--*CCCCHHHCEEEECCCCCCCC-CEE**HHHHHHHHHC*-*H***EEECC*CCEEEECHHHHHHHHHHHCCCC---EEEECCCCCC------------CCCCCCCC*********CCCCC*CEEEEEC------------------------------ --------CCEE***---**CC*EEEEECCCCCCCC***CCCCCCCCCCCCHHHHHHH*-*HHHHCCCC--***CCCCCCC-------CEEECC----------CCC-----------CC------CCCEEEECC---------------------CCCEEEE-C-CCCEEEEEEECC----CC*EEEEEEC-----------HHHHHHCHHHHHHH**----CCCHHH*EEEECCCCCC-C-CEEC*--****-**C-**H***EEE*--CCEEEECHHHHHHHHHHHCCCC---EEEECCCCCC------------CCCCCCCCCCCC------CCCC-CEEEEEC------------------------------ ---------------------------------------------------------------------------------------------------------------------C*****---CCCEEEE*C---------------------CC*EEEE**-CCCEEEEEEECC----CCEEEEEEEC*****-*****HHH*HH*HHHHHHH****-CCCCHHHCEEEE**CCCCC--------------------------*CC-----**CHHHHHHHHHHH********EEE***CCC------------CC******CC------*C****EC***EE**----------------------------- ********CCEE****-***CC*EEEEECCCCCCCC***CCCCCCCCCCCCHHHHHHHHHHHHHH*CCCH****CCCCCCCC------CEEECC----------***CC********CCC------CCCEEEECC---------------------CCCEEEE**-CCCEEEEEEECC----CCEEEEEEEC-----------HHHHH*CHHHHHHH*****CCCCHHHCEEEECCCCCCCC-CEEC*HHHHHHHHHC*******EEE-**CCEEEECHHHHHHHHHHHCCCC***-EEECCCCCC------------CCCCCCCCCCCC*----CCCCCE*EEEE*C*----------------------------- -------------------------------------------------C*HHHHHHHHHHHH**C***H****CCCCCCCC*******EEE************CCCCC**********C********CEEEE**************************EEEE*C*C**EEEEEEE******CC*EEEE**C************------------------------**EEEE****CCCC*C**C*HHHHHHHHH****H******CC*-----*C*HHHHHHHHHH*CC----EEEE***CCC************C*******CCCC**----CC**E*EEEEE******************************* 64438.tem _________________________________ --------CCEE***---**CC*EEEEECCCCCCCC***CCCCCCCCCCCCHHHHHHHHHHHHHHCCCCH****CCCCCCCC------CEEECC----------CCCCC--------CCC------CCCEEEECC---------------------CCCEEEE*C-CCCEEEEEEECC----CCEEEEEEEC-----------HHHHHHCHHHHHHH**---CCCCHHHCEEEECCCCCCCC-CEEC*HHHHHHHHHC***H***EEECC*CCEEEECHHHHHHHHHHHCCCC---EEEECCCCCC------------CCCCCCCCCCCC*----CCCCCECEEEEEC*----------------------------- Structural block scores 0 7 - 4.4 M 67.1 75.0 75.0 4.4 75.0 8 9 C 4.2 M 2.0 5.5 75.0 4.0 75.0 10 11 E 4.2 M 0.5 1.5 75.0 0.0 75.0 12 14 * 3.0 P 3.7 2.0 75.0 3.0 75.0 15 17 - 4.0 M 2.7 75.0 75.0 27.3 75.0 18 19 * 3.0 P 4.5 3.5 75.0 0.5 75.0 20 21 C 4.2 M 6.0 4.0 75.0 10.2 75.0 23 27 E 4.2 M 0.6 0.4 75.0 0.0 75.0 28 35 C 4.2 M 2.9 2.8 75.0 3.4 75.0 36 38 * 3.0 P 5.8 3.7 75.0 5.5 75.0 39 50 C 4.2 M 2.7 3.3 75.0 2.4 63.8 51 64 H 4.4 M 3.2 9.2 75.0 2.6 3.3 65 68 C 4.1 M 4.2 3.6 75.0 3.0 2.8 70 73 * 2.3 P 2.8 21.2 75.0 2.2 2.2 74 81 C 4.4 M 2.9 12.5 75.0 2.5 1.8 82 87 - 4.5 M 75.0 75.0 75.0 75.0 1.7 89 91 E 4.4 M 1.7 2.0 75.0 2.7 0.0 92 93 C 4.1 M 4.0 4.0 75.0 2.0 0.0 94 103 - 4.5 M 75.0 75.0 75.0 75.0 5.3 104 108 C 4.1 M 5.6 34.8 75.0 4.0 4.7 109 116 - 3.8 M 75.0 75.0 75.0 4.0 5.1 117 119 C 4.1 M 4.3 28.7 5.0 2.3 3.0 120 125 - 4.1 M 75.0 75.0 39.3 75.0 6.7 126 128 C 4.7 H 2.0 2.0 4.0 2.3 0.0 129 132 E 5.0 H 0.0 0.0 1.5 0.0 0.0 133 134 C 4.2 M 4.0 6.0 4.5 3.5 0.5 135 155 - 4.5 M 75.0 75.0 75.0 75.0 3.4 156 158 C 4.3 M 5.0 4.0 2.0 0.7 2.0 159 162 E 5.0 H 0.0 0.0 1.5 0.0 0.2 166 168 C 4.7 H 1.0 1.3 1.7 0.7 1.0 169 175 E 5.0 H 0.0 0.0 0.1 0.0 0.4 176 177 C 4.5 M 6.0 5.5 5.0 6.0 3.0 178 181 - 4.5 M 75.0 75.0 75.0 75.0 4.0 182 183 C 5.0 H 3.5 3.5 3.5 3.0 6.5 184 190 E 4.7 H 0.0 0.0 0.0 0.0 0.0 192 202 - 3.9 M 75.0 75.0 12.3 75.0 1.3 203 208 H 4.4 M 2.0 2.7 1.3 2.3 64.2 210 216 H 4.5 M 2.0 2.3 1.7 1.7 75.0 217 218 * 2.1 P 3.5 0.5 1.5 0.0 75.0 219 221 - 3.8 M 52.3 75.0 28.3 5.0 75.0 222 225 C 4.4 M 3.8 23.2 4.0 3.8 75.0 226 228 H 4.5 M 4.7 4.7 4.7 4.3 52.0 230 233 E 5.0 H 0.0 0.0 0.5 0.5 0.0 234 241 C 4.5 M 1.1 10.1 11.4 1.4 2.4 244 245 E 4.1 M 1.5 1.5 75.0 1.0 0.5 248 256 H 4.1 M 3.9 27.7 75.0 3.1 1.0 258 260 * 2.7 P 30.8 30.5 75.0 8.2 1.0 262 264 * 2.1 P 3.0 4.7 75.0 3.7 7.2 265 267 E 4.0 M 4.7 4.7 53.5 4.3 6.5 268 269 C 4.1 M 3.5 41.0 7.8 40.0 3.0 271 272 C 4.2 M 9.2 12.0 75.0 6.5 75.0 273 276 E 4.1 M 2.2 2.2 41.8 1.8 58.2 278 288 H 5.0 H 1.6 1.3 3.3 1.1 1.3 289 292 C 4.2 M 3.5 4.2 3.8 3.0 20.8 293 295 - 3.8 M 75.0 75.0 4.5 6.3 75.0 296 299 E 4.8 H 3.8 2.2 4.0 19.8 0.8 300 305 C 4.4 M 1.8 2.7 4.8 1.7 1.5 306 317 - 4.5 M 75.0 75.0 75.0 75.0 5.6 318 329 C 4.1 M 2.4 3.8 14.1 3.5 2.2 331 334 - 4.2 M 6.4 75.0 57.5 75.0 57.8 335 339 C 4.2 M 3.7 17.0 1.4 2.0 16.6 342 346 E 4.6 H 0.0 0.0 6.0 0.4 0.0 349 377 - 4.5 M 75.0 75.0 75.0 75.0 3.4 >>>>>>