Reading input alignment file to find conserved blocks of secondary structure The input structure based alignment from Comparer _____________________________________________ >P1;d4iuja- ----------CCCCCCCCCCCCCCCCCCCCCCCEEEECCCCCCCCHHHHHCCHHH--CCCEEEEEEEECCCCCHHHHHHHHHHHHHHHHHHHCCCCCEEECCCHHHHHHCCCC-----------------------------CCCCCCHHHHHHHHHHCCCCC-CCCC-----CCCCCCCCCC-----CCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHCCCCEEEEEEEEEEECC---------CCEEEEEEEEEEECCCCCCCCCEEEEEEEEEECCCCCCCHHHHCCCEEEEEEEEEECCCCCCEEEEEEEEEEEEEEEHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCC---------CHHHHHHHHHHHHHHHHHCCCHHHHHHHHHC-CHHHHHHHCC--------CCCCCC-CCC-CCCCCHHHHHHHHHHHCCCC------------ >P1;d5d9aa3 CCHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEECCHHHHCCCCHHHHHHHCCCHHHCCCCCCCCCCC-CHHHHHHHHHHHHHHHHH------CCCCCCCCHHHHHHHCCCCCCCCHHHHHHHHHCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHCCCCCCCCCCCCCCC---------CCCCCCHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHCCCCCCEEEEEEEEEECCCCCCCCCCCEEEEEEEEEEEEECCC---CCCEEEEEEEEECCCC--CCCCCCCCEEEEEEEEECCC--CCCEEEEEEEEEEEEECHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHCEEEEEEECCEEEEEECCCHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHCCCCCCC PSA >P1;d4iuja- ----------67021a454000203000201120224508443425020000064--09424807111619062720250041027007503825752407339105400828-----------------------------6132190045006400551b1-2007-----a810276a89-----285633027300730140300000000030253028008614530100000030518---------6542000000000040509594504000000033305835400430000100416394999626530000013120034604724404410350065027406831885963105107577a1a49---------6105101220040005300629208605721-6068646669--------879b21-504-2044000000203212819a------------ >P1;d5d9aa3 3504733512105219652010301000100222528158850722350032027a915727066917205-636402700630280067------601083ab426513259a9a966898267457577ca59a8a89585221070055017102652a12300539937---------907a773635350454025201300000000001200620370096347410000000407363a7a6c19553510000000000318---9660300000002580--68610440000505716489--a9a55401000031402584046125045008602850243058317859792156015735372937a884414203300223002200220054a20670372365148305114696525789044206603820330000001023014502220577740457 Translating the sequences ----------CCCCCCCCCCCCCCCCCCCCCCCEEEECC****CCHHHHH**HHH--***EEEEEEEECCC*CHHHHHHHHHHHHHHHHH******CEEECCCHHHHHH**CC-----------------------------CCCCCCHHHHHHHHHHCCCCC-CCCC-----*********C-----**HHHHHHHHHHHHH*CCHHHHHHHHHHHHHHHHHHHHHHCCCCEEEEEEEEEEE*C---------C*EEEEEEEEEEE*CCC***CCEEEEEEEEEECCCC**CHHHHCCCEEEEEEEEEECC**CCEEEEEEEEEEEEEEEHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCC*******C*****---------*HHHHHHHHHHHHHHHHHCCCHHHHHHHHH*-*HHHHHHH**--------C*****-***-CCCCCHHHHHHHHHHH****------------ **********CCCCCCCCCCCCCCCCCCCCCCCEEEECCHHHHCC**HHHHHHH***HHH********CCC-CHHHHHHHHHHHHHHHHH------C***CCC*HHHHHHHCC*****************************CCCCCCHHHHHHHHHHCCCCC*CCCC*****---------C*****HHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHCCCC**EEEEEEEEEEC*********CEEEEEEEEEEEEECCC---CC*EEEEEEEEECCCC--C****CCCEEEEEEEEE*CC--CC*EEEEEEEEEEEEE*HHHHHHHH***HHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHCEEEEE*********E***HHHHHHHHHHHHHHCCCHHHHHHHHHH*HHHHHHHHHH********CHHHHH*HHH*CCCCCHHHHHHHHHHHHHHH************ 254132.tem _________________________________ ----------CCCCCCCCCCCCCCCCCCCCCCCEEEECCHHHHCCHHHHHHHHHH--HHHEEEEEEEECCC-CHHHHHHHHHHHHHHHHH------CEEECCCHHHHHHHHCC-----------------------------CCCCCCHHHHHHHHHHCCCCC-CCCC--------------C-----HHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHCCCCEEEEEEEEEEEEC---------CEEEEEEEEEEEEECCC---CCEEEEEEEEEECCCC--CHHHHCCCEEEEEEEEEECC--CCEEEEEEEEEEEEEEEHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHCEEEEE---------EHHHHHHHHHHHHHHHHHCCCHHHHHHHHHH-HHHHHHHHHH--------CHHHHH-HHH-CCCCCHHHHHHHHHHHHHHH------------ Structural block scores 0 9 - 3.0 P 75.0 3.3 10 32 C 5.0 H 2.2 1.8 33 36 E 5.0 H 2.0 4.2 37 38 C 5.0 H 2.5 3.0 39 42 H 3.0 P 4.8 5.2 43 44 C 5.0 H 3.0 4.5 45 54 H 4.0 M 1.7 2.4 55 56 - 3.0 P 75.0 9.8 57 59 H 3.0 P 4.3 4.3 60 67 E 3.0 P 3.0 4.8 68 70 C 5.0 H 5.3 2.3 73 89 H 5.0 H 2.6 3.2 90 95 - 3.0 P 4.2 75.0 97 99 E 3.0 P 2.0 0.3 100 102 C 5.0 H 4.3 7.2 103 110 H 4.2 M 3.4 4.3 111 112 C 5.0 H 5.0 7.0 113 141 - 3.0 P 75.0 7.7 142 147 C 5.0 H 3.7 2.8 148 157 H 5.0 H 1.9 2.1 158 162 C 5.0 H 4.7 4.9 164 167 C 5.0 H 2.2 2.0 168 181 - 3.0 P 30.6 50.4 183 187 - 3.0 P 75.0 6.3 188 203 H 4.6 H 3.1 3.0 204 205 C 5.0 H 2.0 1.5 206 227 H 5.0 H 1.8 1.6 228 231 C 5.0 H 3.2 4.5 232 243 E 4.5 M 0.8 1.2 245 253 - 3.0 P 75.0 7.2 255 267 E 4.7 H 0.8 0.7 268 270 C 5.0 H 3.0 4.0 271 273 - 3.0 P 4.7 75.0 274 275 C 5.0 H 6.5 7.5 276 285 E 4.8 H 0.9 0.9 286 289 C 5.0 H 2.2 3.8 290 291 - 3.0 P 6.5 75.0 293 296 H 3.0 P 2.2 3.8 297 299 C 5.0 H 2.3 2.7 300 309 E 4.8 H 1.5 2.8 310 311 C 5.0 H 6.5 8.5 312 313 - 3.0 P 9.0 75.0 314 315 C 5.0 H 7.5 9.8 316 330 E 4.7 H 1.5 2.4 331 362 H 4.8 H 3.6 3.7 363 366 C 5.0 H 4.8 6.8 367 373 H 3.0 P 3.6 3.6 375 379 E 3.0 P 7.0 5.2 380 388 - 3.0 P 75.0 5.5 390 406 H 4.6 H 1.4 1.2 407 409 C 5.0 H 2.7 3.0 410 419 H 4.8 H 4.0 4.0 421 430 H 4.4 M 5.7 3.2 431 438 - 3.0 P 75.0 6.0 440 444 H 3.0 P 6.1 2.0 446 448 H 3.0 P 3.0 3.0 450 454 C 5.0 H 2.0 1.6 455 469 H 4.5 M 2.6 1.2 470 481 - 3.0 P 75.0 4.2 >>>>>>