Reading input alignment file to find conserved blocks of secondary structure The input structure based alignment from Comparer _____________________________________________ >P1;d1kuta- -----------------------CEEEEEEC--CEEEEEECCC-----------CCCHHHHHHHHHHHC-CHHHHC----------CCCCCEEEEEC----------------------------------------CCEEEECCC------C-CCEEEEEEEECCHHHHHHHCC------------------------------------CCCCEEE----------EEEEEEEECCHHH----------CCCC-CHHHHHHC--CCCC--HHHHHCC-HHHHHHHHHHHHHHHCCCEEEEEEEECEEEC---CCCCEEECCCC-CCCCEEEEEC-----CCC-----------------------CCHHHHHHHHHCCCHHHHHHHHHHHHHCCC >P1;d1w2fa- ---------------CHHHHCCCCCCCEECCCCCEEEEECC------------------HHHHHHHHHCCCHHH------------HHCCCEEEEEEE------------------C-------------------CEEEEEEECCCCCCCCCEEEEEECCCCCCHHHHHHHHHC----------CCEECCCCCCCCCCCCCCHHHHHHCCEECCCCCHHHHHCCHHHHCCEEEEEECCCCCEEC-----CCCCCCCHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHCCCHHHHCEEEECCEEEEEEC---CCCCEEEEEEC-CC-EEEECCC-----------------------CCCCCCCCCCC--CCCCCCCHHHHHHHHHHHHHHHHCC >P1;d2cnqa- CCCCCCCCCCCCEEEECC-----CEEEEEEE-CCEEEEEECCCCEECCEECCCCCCCHHHHHHHHHHHHHHHCCC-----------CCEECCCCCCCC------------------CCHHHHCCHHHHCHHHHHHHCCCEEEEECC------EECCCCEEEEEECCHHHHHHHHH----------HCEECCEECCC-------------CCCCCCEEE----------EEEECCCCCCC------------CCCCCCHHHHHHH----HC--HHHHHHHHHHHHHHHHHHHHHHHHHCEEEEEEEEEEEEE--CCCCEEEEECCCCCCCCEEEEECCCCCCCCCCCCCCCHHH--HHHHHHCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHCCCCC >P1;d3nuaa1 CCC------EEEEEEECC-----CEEEEEECCCCEEEEEECCEEEECCCCEEEECCCHHHHHHHHHHHHHHHHHHC----------CCCCCEEEECC----------------------------------------CCEEEEECC------EECCEEEEEEEEECHHHHHHH------------------------------------CCCCCEEEE----------EEEEEEEECCHHH----------CCCEECHHHHHHC--CCCC--HHHHHHHHHHHHHHHHHHHHHHHCCCEEEEEEEEEEEEE--C--CEEEEECCC-CCCCEEEEECCC------CCCCCCHHH--HCCCC------------------CHHHHHHHHHHHHCC---- >P1;d6cn2a- -----------------------------------------------------CCHHHHHHHHHHHHHHHHHHHC-CCC-CCCHHHHCCEEEEEECCC---CCCCCCCCEEEEECHHHHHHHHHHCCCCHHHHHHHHHCCCEEEC----CEEEECCCCEEEEECCHHHHHHHHHHHHHHHHHHCCCC-CCCCCCEEEEEECCC------CCCEEEEECCCCC-----CCCEEEEECCCCCCCCCCHHHHC-CCCEECHHHHHHHCCCCCCC----CCCCCCHHHHHHHHHHHC-----CCCCCEEEEEECCCC-----------------CCCCCCC------CCCEEEECCCCCC-----------------------HHHHHHHHHCCCCCCCCC >P1;d6ux9a1 -------------------------------------------------------CHHHHHHHHHHHHHHHHHCCCCCCCCCCHHHHHCEEEEEEECCCCCCCCCCCEEEEEEECHHHHHHHHHHCCCCHHHHHHHHHCCCCCCC--CCCEEECCCCCEEEEEECHHHHHHHHHHHHHHHHHHHHCCCCCCCCCEEEEEEEEEC---CEEEEEEEEECCCCCCC---CCCEEEEECCCCCCCCCCHHHHHCCCCEEEHHHHHHCCCCCCCCH--HHHHHHHHHHCCHHHHHHC-----CEECCEEEEEEEEHHHHHCCCCCCCCCCCCCCCEEECCCCCCCCEEEEEEEECCCEECCC-------------------CCCHHHHHHHHHHHHHHHC- PSA >P1;d1kuta- -----------------------9156864b--a404040325-----------735102100100010-700464----------90511136246----------------------------------------541020230------9-160201001120541273686------------------------------------8616708----------8140212233a97----------9451-93850475--a106--4a20654-7203600520450035373202102021020---97671001200-0040050353-----b4a-----------------------8598577626a4722514610610461598 >P1;d1w2fa- ---------------300410912622780c8b21000505------------------840440064070406------------b00051561266------------------b-------------------942001031015b06710000020100001630631677----------393586056384569206881285700260323110610006610000210233766557-----91350564440051058006b2930053016204502710470600540000000000000---73450101002-03-202406b-----------------------a5505035819--4932000004003300600530394 >P1;d2cnqa- 12550606a106345294-----01010317-a91101000010004313062003300200030042008205b-----------2041021b249c------------------47105304a504587036104500000441------64050101000001450283067----------7510083804a-------------906204506----------8020000231a------------6473132950274----09--892074026203700340172058370000002010002--6a58400001000000001003095274458071200210--262057493465950704770065037201501330056819 >P1;d3nuaa1 717------458337435-----212311045b6200020113001684836571a30020001000300820395----------91600035307----------------------------------------731000340------730301020012001710955------------------------------------a2a33590a----------9223201233596----------2334174860295--8107--5a1085027105500610372066250400002000031--9--c51000200-000101010087------652001010--2483a------------------822500530081056---- >P1;d6cn2a- -----------------------------------------------------9573322002300621066269-a75-a0679108446637023b---607413b600210011001200731a164860160006380746----45010344602023086710610270022037014707-911004000000069------d31000120213a-----7042202020379705078a539-d8121303004741600709----549607006300720363-----500600010003269-----------------c23514b------604000250016a-----------------------813700830310182004 >P1;d6ux9a1 -------------------------------------------------------441120023005300660784b73b7056821745542614387844a91127040100011001200740a07287005001764085b--c95602043530203207592071027006701620372907000100000010208---c6411000101020271---802410202018881505883485a31313051069691603049--a419603720600600080-----5004000100000056479c56704046a202002502aa05650000000250054488-------------------b340660073027204815- Translating the sequences -----------------------C***EE**--CEEEEE*C**-----------CC*HHHHHHHHHHH*-*HHH**----------*CC*CEEEE*C----------------------------------------*CEEEE*CC------*-CC**EEEEEEC*HHHHHHH**------------------------------------C*C*EE*----------**EEEEE*CC***----------CCC*-CHHHHHH*--CCCC--HHHHH**-HHHHHHHHHHHH*HH**CEEEE*EEE*EEE*---**C*EEE*CCC-CCCCEEEE*C-----***-----------------------***********C**HHHHHHHHHHH***CC ---------------********C***EE****CEEEEE*C------------------HHHHHHHHH***HHH------------**C*CEEEE***------------------*-------------------***EEEEECC*******E****E*****C*HHHHHHHH*----------*C**CC**C***************CC**C*****************EEEE**CC******-----*CCC**CHHHHHH******C**HHHHHHHHHHHHHHHHHH***HH**CEEEE**EEEEEE*---**C*EEE***C-CC-*EEE**C-----------------------***********--******CHHHHHHHHHHHHH***CC ******************-----C***EE**-*CEEEEE*C*************CC*HHHHHHHHHHHHHHH***-----------*C**C*****C*------------------**********************CEEEEECC------EECC**EEEEEEC*HHHHHHHH*----------*C**CC**C**-------------CCC*C*EE*----------**EE****CCC------------CCC**CHHHHHH*----*C--HHHHHHHHHHHHHHHHHHHH*HH**CEEEE*EEEEEEE*--***C*EEE*CCC*CCCCEEEE*CC****************--************************HHHHHHHHHHHHH***CC ***------*********-----C***EE****CEEEEE*C*************CC*HHHHHHHHHHHHHHHHH**----------*CC*CEEEE*C----------------------------------------*CEEEEECC------EECC**EEEEEE**HHHHHHH------------------------------------CCC*C*EE*----------**EEEEE*CC***----------CCC**CHHHHHH*--CCCC--HHHHHHHHHHHHHHHHHHHH*HH**CEEEE*EEEEEEE*--*--C*EEE*CCC-CCCCEEEE*CC*------*********--*****------------------CHHHHHHHHHHHH**---- -----------------------------------------------------*C**HHHHHHHHHHHHHHHHH*-***-*******CC**EEEE*C*---*************************************C**EEEC----***EECC**EEEEE*C*HHHHHHHH************C-*CC**C*********------CCC***EE*****-----***EEEEE*CCC***********-CCC**CHHHHHH***CCCC*----******HHHHHHHHHHH*-----*****EEEEEE****-----------------*****CC------*************-----------------------HHHHHHHHH*******CC -------------------------------------------------------C*HHHHHHHHHHHHHHHH***************C**EEEE*C*****************************************C*****C--*****E*CC**EEEEEEC*HHHHHHHH************C**CC**C**********---********EE*******---***EEEEE*CCC************CCC***HHHHHH***CCCC**--HHHHHHHHHH**HHHHHH*-----*EE**EEEEEEE******C*****CCC*CCCC*EEE*CC*********************-------------------*C*HHHHHHHHHHHH***C- 56104.tem _________________________________ ---------------***-----C***EE**-*CEEEEE*C**----------*CC*HHHHHHHHHHHHHHHHH**----------*CC*CEEEE*C*------------------**********************CEEEEECC---***EECC**EEEEEEC*HHHHHHHH*----------*C**CC**C*********------CCC*C*EE*****-----***EEEEE*CCC******------CCC**CHHHHHH***CCCC*-HHHHHHHHHHHHHHHHHHHH*HH**CEEEE*EEEEEEE*--***C*EEE*CCC-CCCCEEEE*CC*---************--***-*-------***--******CHHHHHHHHHHHHH***CC Structural block scores 0 14 - 4.3 M 75.0 75.0 3.6 33.0 75.0 75.0 15 17 * 3.4 M 75.0 1.0 5.0 4.0 75.0 75.0 18 22 - 4.5 M 75.0 3.0 75.0 75.0 75.0 75.0 24 26 * 2.7 P 4.0 3.3 0.7 2.0 75.0 75.0 27 28 E 4.3 M 7.0 7.5 1.5 1.0 75.0 75.0 29 30 * 2.7 P 7.8 6.2 4.0 2.0 75.0 75.0 34 38 E 4.3 M 2.4 1.2 0.6 0.8 75.0 75.0 41 42 * 3.4 M 3.5 75.0 0.5 2.0 75.0 75.0 43 52 - 4.1 M 75.0 75.0 1.9 4.1 75.0 75.0 54 55 C 4.2 M 5.0 75.0 1.5 5.8 6.0 39.5 57 73 H 4.7 H 5.4 11.6 1.5 1.1 2.4 2.1 74 75 * 2.6 P 5.0 75.0 43.2 7.0 42.0 6.0 76 85 - 4.1 M 75.0 75.0 75.0 75.0 13.1 6.1 87 88 C 4.3 M 2.5 0.0 2.0 3.5 6.0 5.5 91 94 E 4.5 M 3.0 3.2 4.1 2.8 4.0 3.2 98 115 - 4.2 M 75.0 75.0 75.0 75.0 14.9 3.3 116 137 * 3.2 M 71.8 65.9 3.8 71.9 2.6 2.5 139 143 E 4.3 M 1.0 0.8 0.8 0.8 4.4 4.6 144 145 C 4.7 H 1.5 0.5 2.5 2.0 40.5 43.2 146 148 - 4.2 M 75.0 5.8 75.0 75.0 75.0 32.2 149 151 * 3.4 M 75.0 4.3 75.0 75.0 3.0 3.7 152 153 E 4.2 M 42.0 0.5 5.0 5.0 0.5 1.0 154 155 C 4.5 M 3.5 0.0 2.5 1.5 3.5 3.5 156 157 * 1.0 P 1.0 0.0 0.5 0.5 5.0 4.0 158 163 E 4.5 M 0.5 0.5 0.2 0.8 1.2 1.2 166 173 H 4.9 H 4.5 4.0 3.5 12.9 3.0 3.5 175 184 - 4.1 M 75.0 75.0 75.0 75.0 2.6 3.2 187 188 * 3.0 P 75.0 4.0 0.5 75.0 42.0 3.5 189 190 C 4.3 M 75.0 7.0 4.0 75.0 1.0 0.0 191 192 * 2.7 P 75.0 2.5 5.5 75.0 0.0 0.5 194 202 * 3.2 M 75.0 4.8 59.9 75.0 1.7 0.3 203 208 - 4.3 M 75.0 5.3 75.0 75.0 75.0 41.9 209 211 C 4.2 M 52.7 2.3 5.0 7.7 5.8 2.0 215 216 E 4.5 M 3.5 2.5 2.5 4.5 1.5 0.5 217 221 * 2.9 P 61.6 2.2 61.2 62.1 3.3 1.0 222 226 - 4.3 M 75.0 1.4 75.0 75.0 75.0 46.6 227 229 * 1.8 P 28.0 2.3 27.7 28.7 3.7 3.3 230 234 E 4.6 H 1.8 0.6 0.4 1.6 1.2 1.4 236 238 C 4.5 M 5.5 2.7 4.8 3.7 3.3 3.0 239 244 * 2.9 P 52.7 6.0 75.0 52.5 4.7 4.5 245 250 - 4.1 M 75.0 64.0 75.0 75.0 18.4 6.0 251 253 C 5.0 H 6.0 3.0 5.7 2.7 7.5 4.8 254 255 * 1.4 P 38.0 2.5 2.0 2.5 1.5 2.0 257 262 H 5.0 H 4.5 2.8 4.2 4.8 2.3 3.5 263 265 * 2.6 P 51.7 2.0 51.3 51.7 3.7 5.3 266 269 C 4.4 M 4.4 3.5 39.8 4.0 1.8 2.2 272 291 H 4.6 H 7.0 3.0 3.2 3.3 14.2 10.6 293 294 H 4.3 M 1.5 3.0 2.5 3.0 75.0 75.0 295 296 * 2.7 P 4.0 2.5 5.5 4.0 75.0 75.0 298 301 E 4.3 M 1.8 0.0 0.0 1.0 2.8 2.2 303 309 E 4.8 H 1.0 0.0 0.4 0.7 0.6 0.1 311 312 - 4.1 M 75.0 75.0 75.0 75.0 7.5 2.5 313 315 * 2.9 P 30.3 28.3 7.2 53.0 75.0 5.7 318 320 E 4.2 M 0.3 0.3 0.0 0.3 75.0 6.0 322 324 C 4.3 M 0.7 0.7 0.3 0.7 75.0 2.7 326 329 C 4.4 M 1.0 20.0 0.0 0.2 75.0 3.6 330 333 E 4.3 M 2.0 1.5 0.2 0.5 5.6 1.8 335 336 C 4.7 H 39.0 43.2 4.5 4.0 7.8 6.2 338 340 - 4.1 M 75.0 75.0 4.3 75.0 75.0 3.7 341 352 * 2.8 P 58.4 75.0 2.5 20.0 13.9 1.0 353 354 - 4.1 M 75.0 75.0 75.0 75.0 3.5 4.5 355 357 * 3.2 M 75.0 75.0 3.3 4.7 53.5 6.7 360 366 - 4.1 M 75.0 3.3 5.4 75.0 75.0 75.0 367 369 * 3.4 M 7.3 6.0 4.7 75.0 75.0 75.0 370 371 - 4.1 M 6.5 75.0 3.5 75.0 75.0 75.0 372 377 * 3.3 M 6.4 3.0 4.0 75.0 75.0 64.4 379 391 H 4.7 H 3.0 1.6 1.9 2.4 2.7 2.8 392 394 * 1.6 P 4.0 2.0 6.3 52.0 3.3 4.3 395 396 C 4.4 M 8.5 6.5 5.0 75.0 2.0 40.0 >>>>>>