Reading input alignment file to find conserved blocks of secondary structure The input structure based alignment from Comparer _____________________________________________ >P1;d2ebfx2 CCCHHHHHHHCCCCHHHHHHHCC-----------HHHHHHHHHH--CCCEEEEECC----HHHHHHHHHCHHHHHHC----CCCEEEEEEEEHHHHHHHHHHHHC-CCCCCHHHHHHHHHHCCCCCCCHHHHHHHHHHHC--------CCEEEEEECCCCCC----------------------------------------------------------------------------------------CCCC----CHHHHHHHHHHHHHHHHHHCCCCCCCEEEEECHHHHCCEECC-CCEECCHHHHHC--------CCEEEECC---------------------------------CCCEEECCCC-------HHHCCCCC-------CCC----------------------------- >P1;d2g5gx1 ---------------CCCCCCCEEEEECCCCEECCCCCCCCHHH---CCEEEEEEC-CCCHHHHHHHCCHHHHHHHHHHCCCCEEEEEE-EEHH-HHHHHHHHHHCHHHCCCCCHHHHCCCCCCCCHHHCHHHHHHHHCC--------CCCEEEEECC--HHHHHHHHCCCC-----------------------------------------------CCCCCCCCC------HHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHCC-HHHHHCCCEEEEEEEHHHHCC--------CCCHHHHHHHCCCC-CCEEEEEECCC-------------------------------------------------------------------------CCCH-HHCCEEEEECC------- >P1;d2qgma1 ------CCCCHHHHHHHHHHHHCCCCCC-CCCCCCCHHHHHHHCCCCCCEEEECCCCCCCHHHHCCHHHHHHHHHC-----CCCEEC-C-CCHH-HHHHHHHHHHHCCC----CHHH--CCCCCCCCHH-HHCCCCC-HHHHCCCCCCCCEECCCCCCCCCHHHHHHHHHHHHHHCCCCHHHHHHHHCCHHHCCCCCCCCCCCHHHHHHHHHHHHHHHHHCCCC---------CHHHHHHHHHHHHHHHCCCCC--C-CHHHHHHHHHHHHHHC-CHHHHH-CCCEEECCHHHHCCCCCCCCCCCCCHHHHHHHHHHHHEEEEEEEEEEEEEEECCCCCCCEE-EECCC-CCCCHHHHHHHCCCC-CEEEHHHCCHHHHHHHHCEEEEECCCCC-----CCEEEEEHHHHCCEEEEEEEECCCCCC >P1;d2rada1 ------------CCCCHHHHHCCEECCC-CCCCCCCHHHHHHCCCCCCCEEEEEECCCCCHHHHCCHHHHHHHHHCC----CCCEEEEC-CCHH-HHHHHHHHHHHCCC----CHHH--HCCHHHCCCC-CHHHHHHHHHHHCCCCCCCCEEEC-CCCCCCHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHCCCCCCCC-HHHHHHHHHHCCHHHH-HHHHHH-CCEEEEEEHHHHCCCCC-CCCCCCCHHHHHHHHHHHHEEEEEEEEEEECCCEECCCCCEECCCCCCCCCCCCHHHHCCCCCCCEEEEEHHHCCCHHHHHCCCCEEEECCCCCCCCCCCCEEEECHHHHCCEEEEEEEECCCCCC PSA >P1;d2ebfx2 371860376026a5057605727-----------4761054004--6040000314----75005101831820372----704000002012340682052027-64a9184037304920976891012500410364--------a0602000237529----------------------------------------------------------------------------------------6739----5452425204400710472024b8110000054700103306-962100000206--------00002039---------------------------------8460402507-------a932450b-------7ab----------------------------- >P1;d2g5gx1 ---------------a1639740201206768715396064017---040000004-47284003101007401940386a48000001-0125-23b504704861a80779502820604653829205600340032--------7020001102--693377047849-----------------------------------------------719293005------b9037301630194582548836a3054203010220220-420061921000001361003--------3000010061291a-2711001006a-------------------------------------------------------------------------b233-73011002137------- >P1;d2qgma1 ------b8a9369501720383044152-45185617206207808b04100000002001200102001201035-----902020-1-0000-10130150037285----7156--1055010061-1051523-720758829731200000053047500640151057435a22a5058008701740854a40807883166025203401620457---------725103000300320021239--6-5552142203100300-201812-7730000000000133017a63130002103742893000000000454000265a99254-36046-386000100070439-000303708b403800536220000637-----221360002500000001270520626 >P1;d2rada1 ------------b752910353046072-37192528206306a06a020000000010021000000001000451----90200002-0100-30120141035265----7146--3046113050-360041036107687478302000-10710464006301700473259127504720890251055b304818761656115105300600572487080a3a7031040003002000510506a6-7643332103013002-101442-83001000111001311-74403301011017408750000000024170004259762165060718657000310050928100030450a9616810465120000154228a3455251100600000100270520539 Translating the sequences ****************HHHHHCC-----------**HHHHHHH*--CCCEEEEE*C----HHHH**HHH*HHHHH**----CCCEEEE****HH*HHHHHHHHH*-CCC*****HHH****CCCCCC*H*HHHHHHHHH*--------CCEEE***CCCCC*----------------------------------------------------------------------------------------CCCC----*HHHHHHHHHHHHHH**HH*****CCEEEEE*HHHHCC**C*-CC**CCHHHHH*--------**EEEE**---------------------------------CCC**E****-------HH**C***-------***----------------------------- ---------------******C*****C*CC**CCC*****HH*---CCEEEEE*C-CCCHHHH**H**HHHHHH******CC*EEEE*-**HH-HHHHHHHHHH********CHHH***CCCCCC**H*HHHHHHHH**--------CC*EE***CC--*HHHHHHH****-----------------------------------------------*********------HHHHHHHHHHHHHHHCCCCC*****HHHHHHHHHHHHH**-HHHHH**C*EEEEE*HHHHCC--------CCCHHHHHHH****-**EEEEEE***-------------------------------------------------------------------------***H-HHCCEEEEE**------- ------**********HHHHH*C****C-CC**CCCHHHHHHH***CCCEEEE**C*CCCHHHH**HHHHHHHHH*-----CCCEE*-*-**HH-HHHHHHHHHH*CCC----CHHH--*CCCCCCC*H-HH*****-H*********CCEE****CCCCCHHHHHHH********************************************************---------*HHHHHHHHHHHHHHHCCCCC--*-*HHHHHHHHHHHHHH*-*HHHH*-CC*EEE**HHHHCC**C**CC*CCCHHHHHHH*******EEEEEE****************-*****-************CCC-*E***********HH**C**********-----*******H*HHCCEEEEE********* ------------****HHHHHCC****C-CC**CCCHHHHHH****CCCEEEEE*C*CCCHHHH**HHHHHHHHH**----CCCEEEE*-**HH-HHHHHHHHHH*CCC----CHHH--*CC***CC**-*HHHHHHHH*********CCEEE*-*CCCCCHHHHHHH******************************************************************HHHHHHHHHHHHHHHCCCCC***-*HHHHHHHHH**HHH*-HHHHH*-CCEEEEE*HHHHCC**C-*CC*CCCHHHHHHH*******EEEEEE***********************************CCC**E***********HH**C**********************H*HHCCEEEEE********* 159501.tem _________________________________ ------**********HHHHHCC****C-CC**CCCHHHHHHH***CCCEEEEE*C*CCCHHHH**HHHHHHHHH**----CCCEEEE*-**HH-HHHHHHHHHH*CCC****CHHH***CCCCCCC*H*HHHHHHHHH*********CCEEE***CCCCCHHHHHHH************************************************************-----*HHHHHHHHHHHHHHHCCCCC***-*HHHHHHHHHHHHHH*-HHHHH**CCEEEEE*HHHHCC**C**CC*CCCHHHHHHH*******EEEEEE****************-*****-************CCC**E***********HH**C*************--*******H*HHCCEEEEE********* Structural block scores 0 5 - 4.3 M 4.2 75.0 75.0 75.0 6 15 * 2.9 P 4.5 68.5 6.3 47.5 16 20 H 4.3 M 5.0 5.2 4.0 3.6 21 22 C 4.3 M 4.5 2.0 1.5 1.5 23 26 * 2.3 P 75.0 1.2 3.5 4.2 29 30 C 4.3 M 75.0 6.5 4.5 5.0 31 32 * 2.3 P 75.0 7.5 4.5 5.0 33 35 C 4.3 M 28.7 3.0 4.0 3.0 36 42 H 4.4 M 2.3 3.7 3.4 3.6 43 45 * 2.7 P 51.3 52.3 5.3 5.5 46 48 C 4.8 H 3.3 26.3 5.2 4.2 49 53 E 4.9 H 0.6 0.0 0.2 0.0 57 59 C 4.3 M 75.0 4.3 0.7 0.3 60 63 H 5.0 H 3.0 3.0 0.8 0.8 64 65 * 1.0 P 3.0 2.0 0.5 0.0 66 74 H 4.8 H 2.9 2.4 1.0 0.6 75 76 * 1.6 P 4.5 2.0 40.0 3.0 77 80 - 4.3 M 75.0 6.9 75.0 75.0 81 83 C 4.8 H 3.7 4.0 3.7 3.7 84 87 E 4.7 H 0.0 0.0 19.2 0.0 90 91 * 1.0 P 0.5 0.5 0.0 0.5 92 93 H 5.0 H 2.5 3.5 0.0 0.0 95 104 H 4.9 H 3.2 4.5 1.4 1.5 106 108 C 4.3 M 6.8 6.5 5.0 4.3 109 112 * 3.5 M 5.5 5.8 75.0 75.0 114 116 H 5.0 H 4.3 3.3 4.0 3.7 117 119 * 2.7 P 4.3 2.7 50.3 51.0 120 126 C 4.5 M 5.9 4.0 1.6 2.1 130 138 H 4.4 M 2.3 2.3 11.0 2.6 139 147 * 3.2 M 67.1 66.9 5.3 5.3 148 149 C 5.0 H 5.2 3.5 2.0 1.5 150 152 E 4.5 M 2.7 0.7 0.7 0.7 153 155 * 1.4 P 0.0 0.7 0.0 25.3 156 160 C 4.6 H 3.8 31.6 2.4 2.4 161 167 H 4.3 M 65.6 4.7 3.1 2.7 168 227 * 3.3 M 75.0 59.8 8.7 3.7 228 232 - 4.3 M 75.0 75.0 75.0 6.4 234 248 H 4.3 M 75.0 4.2 1.3 0.9 249 253 C 4.9 H 20.0 5.4 3.4 2.2 254 256 * 3.1 M 75.0 5.7 52.0 7.5 259 272 H 4.8 H 2.9 1.6 2.0 2.1 275 279 H 4.4 M 3.0 2.4 2.4 2.0 280 281 * 2.2 P 9.8 5.0 38.5 38.5 282 283 C 4.7 H 1.0 1.5 7.0 5.5 284 288 E 4.7 H 0.0 0.0 0.6 0.2 290 293 H 5.0 H 2.8 2.5 0.0 0.8 294 295 C 5.0 H 0.5 1.5 0.5 0.5 296 297 * 2.3 P 3.0 75.0 3.0 2.0 299 300 * 3.5 M 40.5 75.0 4.0 41.0 301 302 C 4.3 M 7.5 75.0 8.2 4.0 304 306 C 4.8 H 0.3 1.0 1.3 2.0 307 313 H 4.8 H 11.9 1.1 1.9 1.6 314 320 * 2.5 P 75.0 15.2 3.7 3.4 321 326 E 4.8 H 0.3 0.5 0.0 0.0 327 342 * 3.1 M 66.4 62.0 4.1 3.5 344 348 * 3.5 M 75.0 75.0 3.8 2.8 350 361 * 3.5 M 75.0 75.0 2.1 2.2 362 364 C 4.3 M 6.0 75.0 5.3 6.3 365 366 * 2.9 P 2.0 75.0 37.5 0.5 368 378 * 3.1 M 49.0 75.0 3.6 4.0 379 380 H 4.3 M 9.8 75.0 4.0 4.5 381 382 * 2.3 P 2.5 75.0 2.5 2.0 384 396 * 3.2 M 43.9 75.0 19.3 2.3 397 398 - 4.3 M 75.0 75.0 75.0 6.8 399 405 * 3.0 P 75.0 45.2 2.0 3.3 408 409 H 4.3 M 75.0 5.0 2.5 3.0 410 411 C 4.3 M 75.0 0.5 0.0 0.0 412 416 E 4.3 M 75.0 0.8 0.2 0.2 417 425 * 3.2 M 75.0 59.4 3.3 3.7 >>>>>>