Reading input alignment file to find conserved blocks of secondary structure The input structure based alignment from Comparer _____________________________________________ >P1;d1olta- CCCCCCCCCCCCCCCCCCHHHCCCCCCHHHHHHHHCCC--CCCCEEEEEEECEE---CCCCCCCCCCCEECC----CCHHHHHHHHHHHHHHHHHHHHHCCCCEEEEEEEECCHHHC-CHHHHHHHHHHHHHHCCEEEEEEEEEEECCCCCCCHHHHHHHHCCCCEEEEEEECCCHHHHHH-HCCCCCHHHHHHHHHHHHHCCCCCCEEEEEECCCCCCHHHHHHHHHHHHHH--CCCEEEEEECCCCCCCCHHHHHCCHHHCCCHHHHHHHHHHHHHHHHHC--------CCEEEECCEEE-CCC--CHHHHHHHHCCCEECC---CCEECCCCCEEEEECCCCEEEECCEEEEECCCHHHHHHHHHHHCCCEEEEEECCHHHHHHHHHHHHHHHHCEEEHHHHHHHCCCCHHHHCHHHHHHHHHHHHCCCEEECCCEEEECCCCHHHHHHHHHCCCCCC >P1;d1r30a- C--CCCCCCCHHHH------HCCHHHHHHHHHHHHHHHCCCCCCEEEEEEEEECCCCCCCCCCCCCCCCCCC----CCCCCCCCHHHHHHHHHHHHHC----CCCEEEEEECCCCCCCCHHHHHHHHHHHHHC-----CCEEEEECCC--CCHHHHHHHHHHCCCEEECCCCC-CHHHHHH-HCCCCCHHHHHHHHHHHHHHHC-EEECCEEECC-CCCHHHHHHHHHHHHCCCCCCCEEEEEECCCCC--CCCCCCCC---CCCHHHHHHHHHHHHHHCC----------CCEEEEE--CC-HHHCCHHHHHHHHHHCCCEEE-----CCC--------CCCCCCCCC----------HHHHHHHHHHCCCCCCCC------------------------------------------------------------------------------------ >P1;d1tv8a- -----------------------------------CCCCCCCCCCCCEEEEECCCCCCCCCCCCCCCCCCCCCCCCCCHHHCCCHHHHHHHHHHHHHC----CCCEEEEECCCHHHCC---CHHHHHHHHCCCC----CCCEEEEEECCCCHHHHHHHHHHHCCCEEEEECCCCCHHHHHHHHCCCCCHHHHHHHHHHHHHCCC-EEEEEEEECC-CCCHHHHHHHHHHHHH--CCCCEEEEECCCCCC-----------CCCCC-CCCCCCHHHHHHHHHHHCCEEEECCCCCCCCCEEEEEC-----------CCCCEEEEECCCCCCCHHHCCEEEECCCCCEECCCCCCCCCCCHHHHHHC----------------CCCHHHHHHHHHHHHHCCC---------CCHHHHHHHHHHHHCC------------------------------------ PSA >P1;d1olta- 3905036a1192161003492066a0848303801842--68240002000001---143120136313216----645306500610350055006308b0602101000000000-7490043007104630704ba020102010150846105203826042010100004560083-030607383015005203827081010201000040409206900730360--5021010460916286361066087a2206964233024500520382--------90300003100-359--1300411574603121---5300331800000000101020020000014718503510966010022016085400002200330001050708612a71a07068305702870641184700825a810402440110052004000436 >P1;d1r30a- b--72639503710------837196007402610584173640100111001008163113121006520d----2955923718601430571484----6060000001160879204502600640491-----7030002032--04881063018120200203000-0271097-00521717411500620290a0-4000001010-80676110100130021662030000210222a--60312b2b---8175640010000001002----------7030000--20-035073800230050000001-----016--------713117008----------4a403700653710743a------------------------------------------------------------------------------------ >P1;d1tv8a- -----------------------------------970506470305202010023120026360359623ca3912679400618202300400040----3034020200000308---602500530590b----606300020102205730550262205601050101639203710339260540160043037180-7030102016-a302800240063018--36010102013423c-----------66003-383002186028405861a0672a657a4040401507-----------5231200010002703194213020113010102433a983450163037----------------a054860382045104707---------443124156318637a------------------------------------ Translating the sequences C**CCCCCCC**********HCC****HHHHHHHHCCC--CCCCEEEEEEE*E*---CCCCCCCCCCC**CC----CCHHH***HHHHHHHHHHHHH*****C**EEEEEECCHHHC-CHHHHHHHHHHHHH*C******EEEEEECCCCCC*HHHHHHHH*CCCEEEEE**CCCHHHHHH-HCCCCCHHHHHHHHHHHHHCCC***EEEEEECC*CCCHHHHHHHHHHHHH*--CCCEEEEEECCCCC**C*****CC***CCCHHHHHHHHHHHHHHHHH*--------CCEEEEC*EEE-C**--*HHHHHHHHCCCEE**---CC**C**CCEEEE*CCCCEE**CC*****CC*HHHHHHHHHH*CCC***********HHHHHHHHHHHHHC***********CC*HHHH*HHHHHH************************************** C--CCCCCCC****------HCC****HHHHHHHH***CCCCCCEEEEEEEEECCCCCCCCCCCCCCCCCCC----CC***CCCHHHHHHHHHHHHHC----CCCEEEEEECC***CCCHHHHHHHHHHHHHC-----CCEEEEE*CC--CCHHHHHHHHHHCCCEEE**CCC-CHHHHHH-HCCCCCHHHHHHHHHHHHH**C-EEE**EEECC-CCCHHHHHHHHHHHH***CCCCEEEEEECCCCC--C*****CC---CCCHHHHHHHHHHHHHH**----------CCEEEE*--**-******HHHHHHHH*CC*EEE-----CCC--------CCCCC**CC----------HHHHHHHHHH*CCC****------------------------------------------------------------------------------------ -----------------------------------CCCCCCCCC***EEEEE*CCCCCCCCCCCCCCCCCCC****CCHHHCCCHHHHHHHHHHHHHC----CCCEEEEE*CCHHHCC---*HHHHHHHH**CC----CC*EEEEE*CCCC*HHHHHHHHHHCCCEEEEECCCCCHHHHHH*HCCCCCHHHHHHHHHHHHHCCC-EEEEEEEECC-CCCHHHHHHHHHHHHH--CCCCEEEEE*CCCCC-----------**CCC-******HHHHHHHHHH*********CC****C*EEE*C-----------**CC*EEEE***CCCC***CCEEEECCCCCEECCCC*****CC*HHHHH*----------------***HHHHHHHHHHHHHC**---------CC*HHHH*HHHHHH**------------------------------------ 102114.tem _________________________________ C--CCCCCCC****------HCC****HHHHHHHHCCCCCCCCCEEEEEEEEECCCCCCCCCCCCCCCCCCC----CCHHHCCCHHHHHHHHHHHHHC----CCCEEEEEECCHHHCCCHHHHHHHHHHHHHCC----CCEEEEEECCCCCCHHHHHHHHHHCCCEEEEECCCCCHHHHHH-HCCCCCHHHHHHHHHHHHHCCC-EEEEEEEECC-CCCHHHHHHHHHHHHH*-CCCCEEEEEECCCCC--C*****CC-**CCCHHHHHHHHHHHHHHHHH*--------CCEEEEC*EEE-C**--*HHHHHHHHCCCEEEE---CCCCC**CCEEEECCCCCEECCCC*****CC*HHHHHHHHHH*CCC****----***HHHHHHHHHHHHHC**---------CC*HHHH*HHHHHH**------------------------------------ Structural block scores 1 2 - 4.0 M 4.5 75.0 75.0 3 9 C 4.0 M 3.8 4.6 75.0 10 13 * 2.7 P 4.5 2.8 75.0 14 19 - 4.0 M 2.8 75.0 75.0 21 22 C 4.0 M 3.0 5.0 75.0 23 26 * 2.7 P 6.1 4.0 75.0 27 34 H 4.0 M 3.4 2.5 75.0 35 43 C 4.4 M 20.4 4.2 4.2 44 52 E 4.4 M 0.2 0.6 1.4 53 71 C 4.7 H 13.8 2.8 3.4 72 75 - 4.0 M 75.0 75.0 5.9 76 77 C 5.0 H 5.0 5.5 4.0 78 80 H 4.0 M 2.7 6.3 6.7 81 83 C 4.0 M 3.7 4.0 2.0 84 96 H 5.0 H 2.4 3.7 1.8 98 101 - 4.0 M 4.9 75.0 75.0 102 104 C 4.3 M 2.7 4.0 2.0 105 110 E 4.8 H 0.3 0.0 1.3 111 112 C 5.0 H 0.0 1.0 0.0 113 115 H 4.0 M 0.0 4.7 1.0 116 118 C 4.3 M 27.3 6.0 27.7 119 131 H 4.6 H 2.9 3.1 14.2 132 133 C 4.0 M 1.5 38.0 5.8 134 137 - 4.0 M 5.6 75.0 75.0 138 139 C 4.0 M 5.2 3.5 3.0 140 145 E 4.7 H 0.8 0.8 1.8 146 151 C 4.3 M 2.5 26.5 0.8 152 161 H 4.8 H 3.1 3.6 3.5 162 164 C 5.0 H 3.3 1.3 2.3 165 169 E 4.6 H 0.8 1.0 2.4 170 174 C 4.4 M 0.8 15.0 1.6 175 180 H 5.0 H 3.7 4.3 4.0 183 187 C 5.0 H 3.2 3.0 4.6 188 200 H 5.0 H 2.9 2.9 2.5 201 203 C 4.3 M 3.0 3.5 3.0 205 212 E 4.5 M 0.6 0.6 1.6 213 214 C 5.0 H 0.0 0.5 3.5 216 218 C 5.0 H 2.7 4.7 4.5 219 231 H 4.9 H 3.5 1.7 2.6 234 237 C 4.8 H 20.5 2.8 2.5 238 243 E 4.8 H 2.0 0.5 0.7 244 248 C 5.0 H 3.6 3.3 4.9 249 250 - 4.0 M 7.0 75.0 75.0 252 256 * 2.7 P 3.8 3.5 75.0 257 258 C 4.0 M 4.0 6.8 75.0 260 261 * 2.7 P 6.2 75.0 6.0 262 264 C 5.0 H 2.7 5.3 1.0 265 281 H 4.4 M 3.3 5.5 7.8 283 290 - 4.0 M 75.0 75.0 5.4 291 292 C 5.0 H 4.5 3.5 6.0 293 296 E 4.0 M 0.8 0.8 4.6 299 301 E 4.0 M 0.3 25.7 2.0 304 305 * 2.7 P 7.0 4.0 75.0 306 307 - 4.0 M 75.0 3.5 75.0 309 316 H 4.0 M 2.6 2.2 57.1 317 319 C 4.3 M 3.3 0.0 2.0 320 323 E 4.2 M 1.8 0.2 0.2 324 326 - 4.0 M 75.0 75.0 0.0 327 331 C 4.0 M 2.2 31.4 2.6 332 333 * 2.7 P 2.0 75.0 6.5 334 335 C 4.0 M 4.0 75.0 1.5 336 339 E 4.0 M 0.0 75.0 1.2 340 344 C 4.8 H 0.2 2.6 1.2 345 346 E 4.0 M 0.5 3.5 0.5 347 350 C 4.0 M 1.0 39.5 2.2 351 355 * 2.7 P 0.0 75.0 6.7 356 357 C 4.0 M 2.5 75.0 4.5 359 368 H 4.5 M 3.8 4.0 32.0 370 372 C 4.0 M 0.3 2.7 75.0 373 376 * 2.7 P 1.0 6.1 75.0 377 380 - 4.0 M 3.8 75.0 75.0 381 383 * 2.7 P 3.0 75.0 5.2 384 396 H 4.0 M 0.8 75.0 3.5 398 399 * 2.7 P 2.5 75.0 3.5 400 408 - 4.0 M 4.7 75.0 75.0 409 410 C 4.0 M 5.2 75.0 4.0 412 415 H 4.0 M 4.2 75.0 2.0 417 422 H 4.0 M 4.8 75.0 4.5 423 424 * 2.7 P 3.0 75.0 8.8 425 460 - 4.0 M 2.8 75.0 75.0 >>>>>>