Reading input alignment file to find conserved blocks of secondary structure The input structure based alignment from Comparer _____________________________________________ >P1;d1f08a1 --------------------------------------------------CCHHHHHHHHHHHCCCHHH--CCCCCCCCCCCEEEEEEEEECCC------------------HHHHHHHHHHHHCC--------------E-EEEEEEEEEEC-----CEEEEEEEEEEEEEECHHHHHHHHHHHHCC--CHHHEEEECC--CC-----CCHHHHHHHHHHCCCC--------------------------------------------CCEEEE-----CCCHHHHHHCCCC--------- >P1;d1m55a- CCEEEEEEEECCC---------CCCCCCCCCC---------------------HHHHHHHH-------HCCCCCCC-------------------CCCCCHHHCCHHHHHHHHHHHHHHHHHHHHHHC-----------CCCCEEEEEEECC-------CCEEEEEEEECC---------------CCC------------------HHHHHHHHHHHHHHHHHHCCC-CCCCCCC-CCEEECCCCCCCCCCCEECCHHHHHCCCCCCCCEEEEEECCHHHCCHHHCHHHHHHHHHHHHHCC >P1;d1p4da- --CEEEEECC--CHHHHHHHHHCHHHCCCCCCCCCEEECHHHHHCCCCCCCCHHHHHHHHCCCCC--CCCCCCCEECCEECCCCEEEEEEECCHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHCCCEEEEEECCEEEEEECCCCCEEEEEEEECCCCCEEEEEEEEEECCEEEC-----------CEEECC-CCCCCCCCCHHHHHHHCHHHHHHHHHHHHHHHHHHCCCCCEECCCCCCEECCCCCHHHHCCCHHHHHHHHHHH-HHCCCCC--------HHHHHHHHHHHHHHHHCCCC >P1;d1r9wa- --------------------------------------------------CHHHHHHHHHHHHCCCHHH--CCC-------CEEEEEEEEEEEC------------------HHHHHCHHHHHHHH--------------E-EEEEEEEEEEC-----CEEEEEEEEEEEEEECHHHHHHHHHHHHCC--CHHHEEEECC--CC-----CCHHHHHHHHHHHHCC--------------------------------------------CCEEEE-----CCCHHHHHHCCCC--------- >P1;d3l57a- --CEEEEEEECCCHHHCCCCCCCCCCCCC--CCCEEEECHHHHHCCCCCCCCHHHHHHHHCCEEE--CCEECCC---CCCCCEEEEEEEEECCHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHCCCEEEEC----CEEEECCCCCEEEEEEEE---CCCEEEEEEEEECCEECCC----------CCEECC-C---------CHHHHCCHHHHHHHHHHHHHHHHHHHCCCEEEECC-CEEEECC-------------------------------------------------------- >P1;d4nbpa- ---------------------------------------------------CCCCCHHHHHH--CCCCC--C---------CCCEEEEEEEEE-------------------HHHHHHHHHHHHHH--------------C-CCCEEEEEEEC-----C--EEEEEEEEEEEECHHHHHHHHHCCCC----CCCEEEEEC--C----------CHHHHHHHCCCC--------------------------------------------CCEEEEECCCCCCCHHHCCCC------------ >P1;d6q1ma- ------------------------------------------------------------------------------CCEEEEEEEEEEECCCC---------------CHHHHHHHHHHHCHHH--------------CCCEEEEEEEECC----CCCEEEEEEEEEEEEEE--CCCCCCC--EECCCCCCCEECCEEEECC-----CHHHHHHHHHCCCCCCC-------------------------------------------CCEEEECCCCCC--------------------- PSA >P1;d1f08a1 --------------------------------------------------2689238206600833067--00472a74755253000001907------------------78406601650373--------------0-7000012543a-----9640000000068421056039301a1081--7571000200--45-----876a005105811759--------------------------------------------903535-----a31710541069d--------- >P1;d1m55a- 7650000303003---------4587104a07---------------------a7058217-------84818249-------------------905063940434100001400410071026109-----------4804100000439-------831100000125---------------807------------------592086104403730064004-5270609-800503458ab381341513200350031805400001021960550011381086037537876 >P1;d1p4da- --60607805--82b70083016853140088191202060076091688075720350020302--5a34206569a72606101001010210000000009083026002500530063007200013579973613704200000000011a8520300010000000219-----------870230-3267b77640353057436600440052016304720050664795250202a01293077517713770473-0872a17--------1961264068227858858a >P1;d1r9wa- --------------------------------------------------8796037006910813065--004-------6341000000107------------------69309704740565--------------0-60000025807-----470000000304922536500690381070--6384000320--34-----924800420451164c--------------------------------------------605226-----a30710673085c--------- >P1;d3l57a- --308063024550780103829b78515--67403021600731817a3040720340030206--7955090---fa7735000001030264004200366285016002500310062006201063e----883280700000000426---7804010100000003196----------660430-2---------143027249501310163017206839280667b8-9304108-------------------------------------------------------- >P1;d4nbpa- ---------------------------------------------------62501a60682--02473--9---------784540000003-------------------57204501660265--------------1-8060000023c-----b--30000010386241350481046208----a31020100--6----------432400210269--------------------------------------------407244125b90077952a88------------ >P1;d6q1ma- ------------------------------------------------------------------------------37142410102057061---------------5057005404740881--------------706000001125a----88110000000075060--6746402--152a786645150705409-----60760363018608184-------------------------------------------b20434a33a2b--------------------- Translating the sequences --------------------------------------------------***HHHHHHH*********--CCC*******C**EEEEEEE***------------------HHHHHHHHHHHH**--------------*-***EEEEEEE*-----C*EEEEEEEEE**EE*************CC--C*********--**-----C*HHHHHHHHHH****--------------------------------------------CCEEEE-----***HHH*******--------- *************---------**********---------------------HHHHHHH*-------***CCC**-------------------*****************HHHHHHHHHHHH****-----------***C**EEEEE**-------**EEEEEEEE**---------------CC*------------------****HHHHHHHHHH*******-*******-********************************C*EEEE********HHH**************** --********--*****************************************HHHHHHH*****--****CCC*******C**EEEEEEE*********************HHHHHHHHHHHH******************C***EEEEEE******C*EEEEEEEEE**EE**-----------C***C*-****************C*HHHHHHHHHH*********************************************-**CC***--------*HHH**************** --------------------------------------------------***HHHHHHH*********--CCC-------C**EEEEEEE***------------------HHHHH*HHHHHH**--------------*-***EEEEEEE*-----C*EEEEEEEEE**EE*************CC--C*********--**-----C*HHHHHHHHHH****--------------------------------------------CCEEEE-----***HHH*******--------- --***************************--**********************HHHHHHH*****--****CCC---****C**EEEEEEE*********************HHHHHHHHHHHH********----******C***EEEEEE**---*C*EEEEEEEEE**EE***----------CC**C*-*---------******C*HHHHHHHHHH*****************-*******-------------------------------------------------------- ---------------------------------------------------*****HHHH**--*****--C---------C**EEEEEEE**-------------------HHHHHHHHHHHH**--------------*-C**EEEEEEE*-----C--EEEEEEEE**EE*************C----*********--*----------*HHHHHHH****--------------------------------------------CCEEEE********HHH****------------ ------------------------------------------------------------------------------******EEEEEEE****---------------**HHHHHHHHHH*H**--------------**C**EEEEEE**----*C*EEEEEEEEE**EE*--*******--**C**C*************-----C*HHHHHHHH*******-------------------------------------------CCEEEE******--------------------- 55464.tem _________________________________ --********--*---------*******--*------------------***HHHHHHH***********CCC**-****C**EEEEEEE*********************HHHHHHHHHHHH****-----------***C**EEEEEEE*----*C*EEEEEEEEE**EE*************CC**C*********--**---**C*HHHHHHHHHH*******-*******-*-*******-----------------------CCEEEE********HHH*******--------- Structural block scores 0 1 - 4.6 H 75.0 6.5 75.0 75.0 75.0 75.0 75.0 2 9 * 3.7 M 75.0 1.4 4.0 75.0 2.8 75.0 75.0 10 11 - 4.2 M 75.0 0.0 75.0 75.0 4.5 75.0 75.0 13 21 - 4.2 M 75.0 75.0 3.6 75.0 3.2 75.0 75.0 22 28 * 3.7 M 75.0 4.1 3.9 75.0 6.6 75.0 75.0 29 30 - 4.2 M 75.0 5.2 4.0 75.0 75.0 75.0 75.0 32 49 - 4.2 M 75.0 75.0 3.7 75.0 3.5 75.0 75.0 50 52 * 2.7 P 5.3 75.0 4.0 8.0 1.3 27.7 75.0 53 59 H 4.5 M 4.3 4.8 2.4 3.1 2.3 4.1 75.0 60 70 * 2.9 P 16.6 50.2 16.3 16.6 17.0 29.6 75.0 71 73 C 4.5 M 1.3 3.7 2.7 1.3 3.0 53.0 75.0 74 75 * 3.7 M 4.5 6.5 5.5 75.0 75.0 75.0 75.0 77 80 * 3.2 M 5.8 75.0 6.4 75.0 11.8 75.0 21.5 82 83 * 1.8 P 3.5 75.0 3.5 3.5 2.5 6.0 3.0 84 90 E 4.6 H 0.6 75.0 0.4 0.1 0.6 1.3 1.3 91 111 * 3.4 M 65.0 16.6 1.5 64.7 2.6 68.0 54.5 112 123 H 4.9 H 3.8 1.7 2.0 4.5 1.6 3.2 3.7 124 127 * 2.4 P 40.0 4.0 2.2 40.2 2.2 40.2 39.8 128 138 - 4.3 M 75.0 75.0 4.6 75.0 31.1 75.0 75.0 139 141 * 2.6 P 50.0 4.0 3.3 50.0 3.3 50.3 27.3 143 144 * 1.0 P 0.0 0.5 1.0 0.0 0.0 3.0 0.0 145 151 E 4.7 H 2.1 2.3 0.0 2.1 0.6 0.7 1.3 153 156 - 4.5 M 75.0 75.0 5.1 75.0 57.8 75.0 75.0 160 168 E 4.9 H 0.4 0.7 0.4 0.3 0.7 8.8 0.1 169 170 * 1.0 P 7.0 3.5 0.0 6.5 0.0 5.5 6.0 171 172 E 4.6 H 3.0 75.0 1.0 2.0 1.5 4.0 3.0 173 185 * 3.0 P 3.0 75.0 64.2 3.5 58.9 2.9 25.4 186 187 C 4.4 M 4.5 4.0 7.5 3.5 6.0 41.5 3.5 188 189 * 3.4 M 75.0 41.0 1.0 75.0 2.0 75.0 8.8 191 199 * 2.4 P 1.7 75.0 13.2 2.2 58.6 1.9 3.8 200 201 - 4.2 M 75.0 75.0 5.0 75.0 75.0 75.0 4.5 202 203 * 2.5 P 4.5 75.0 1.5 3.5 38.0 40.5 4.5 204 206 - 4.2 M 75.0 75.0 2.7 75.0 2.3 75.0 75.0 207 208 * 3.7 M 75.0 7.0 6.0 75.0 4.5 75.0 75.0 211 220 H 4.8 H 3.6 3.6 2.7 2.8 2.9 16.6 4.0 221 227 * 2.1 P 35.3 2.0 3.0 35.5 3.4 34.6 24.4 229 235 * 3.7 M 75.0 4.1 3.0 75.0 5.4 75.0 75.0 239 245 * 3.7 M 75.0 3.6 3.1 75.0 3.6 75.0 75.0 246 268 - 4.2 M 75.0 3.4 7.1 75.0 75.0 75.0 75.0 269 270 C 4.4 M 4.5 2.0 4.5 3.0 75.0 2.0 6.8 271 274 E 4.3 M 4.0 0.2 23.4 3.8 75.0 4.2 2.8 275 282 * 3.3 M 48.7 3.5 65.8 48.6 75.0 4.4 23.8 283 285 H 4.4 M 2.7 0.3 5.3 2.7 75.0 7.0 75.0 286 292 * 2.8 P 5.5 3.9 4.0 5.9 75.0 36.2 75.0 293 301 - 4.2 M 75.0 5.1 6.8 75.0 75.0 75.0 75.0 >>>>>>