Reading input alignment file to find conserved blocks of secondary structure The input structure based alignment from Comparer _____________________________________________ >P1;d1h3za- ------------------------------CCCCCCCCCEEEEEEEC---C--EEEEEEEECCCCCCCHHHHCCCCCC-----CCCCEEEEECCCCE----EEEECCC--CEEEC-CHHHHHHHHH-----CCCCCCHHHHHHHHHHCCCCCCCCCCCCC----------------------------- >P1;d1khca- ------------------------------CCC-CCCCCCEEEEECC---C---CEEEEEEECCCCCCCCCCC------------CEEEEEECCCCC----EEEEEHH--HCEE--CC-CHHHHCC-----HHHHCCHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCHHHHHHHHHCCCCCCCCCCC >P1;d1mhna- --------------------------------CCCCCCCCEEEEECC---CC-CCEEEEEEEEEECC-----------------CCEEEEEECCCCE----EEEEEHH--HCCCC-CCC---------------------------------------------------------------------- >P1;d1oz2a1 CCCCHHHHHHHHCCCCCCHHHCCHHHHCCCCCC-CCCCCCEEEEEEC---CEEEEEEEEEEEEEE-------------------CCEEEEEECCC--CHHHCEEEECCCCCEEC---CCHHHHHCCCEECCC-CC------CCCC-------------------------------------------- >P1;d1oz2a2 --CCHHHHHHHHCCCCCCHHHCC--CCCCCCCCCCCCCCCEEEEECC---CCCCCEEEEEEEEEE-------------------CCEEEEEECCC--CHHHCEEECCCCCCEEC---CCHHHHHCCCEECCC-CCC-----CCCC-------------------------------------------- >P1;d1wjra1 -------------------------------CCCCCCCCCEEEEECC---CCCCEEEEEEEEEEE-------------------CCEEEEEECCCCCCCCCEEEEECCCCCCCC---CCCCCCCCCEECCCCCCCCCCCHHHHHHHHHHHHHHHCCCCCCHHHHCCCCCC------------------- >P1;d2g3ra1 -----------------------------------CCCCCEEEEECC---CC-CCEEEEEEEEEEEC------------------CEEEEEEC-CCC----EEEEEHH--HEECC-CC----------------------------------------------------------------------- >P1;d2hqxa1 --------------CHHHHHHHHHHHHHHCC---CCCCC-CEEEEC-CC----CCEEEEEEEEEEEC------------------CEEEEEECCCCC----EEEECHH--HEECCC---HHHCCCCCCCC----------------------------------------------------------- >P1;d2jnga1 ------------------CCCCCCCCHHHHHHHHHCCCCCEEEECCCCCCCCCCCEEEEEEEC------------------CCC-CEEEEEECCCCE----EEEEEHH--HEEEEE--CCC-------------------------------------------------------------------- >P1;d2l89a- ------------------------------CCCCCCCCCEEEEEEEC---C--EEEEEEEEEEE-EEE------CCCCCCCCCCEEEEEEEECCCCE----EEEECHH--HEEEC-CHHHHHHHHC-----CCCCCCHHHHHHHHHHCCCCCCCCCCCCCCC--------------------------- >P1;d2l8da1 ------------------------------CCCCCCCCCCEEEEECC---CC-CCEEEEEEEEEECC-----------------CCEEEEEEC-CCC----EEEEEHH--HEECC-CCCC--------------------------------------------------------------------C >P1;d3fdra- ---------------CCC-CC-CCHHHHCCCCCCCCCCCCEEEEECCCC----CCEEEEEEEEECCC------------------CCEEEEECCCC-----CEEECC---CCEECC---HHHH-CCCCCCCC--------------------------------------------------------- >P1;d4rxja- -----------------------------------CCCCCEEEEEE------CCEEEEEEECCCCCC----------CCCCCCCCCEECEEECCCCC-----CCEEHH--HCEECCCCCHHHHHHHCCCCHH-------------------------------------HHHHHHHHHHHHHHCCCCCC >P1;d6iipa1 ----------------------------------CCCCCCEEEECCC---C--CCCEEEEECCCCCCCCCCCC------------CCEEEEECCCCC----EEEECHH--HEEE--HHHHHHHHCC-------CCCCHHHHHHHHHHHHCCCC------------------------------------ PSA >P1;d1h3za- ------------------------------bb74b06503202043b---d--5330000006492028905954198-----ba922100001a46----020042a--20330-7684056126-----6175729702700640270561b409355----------------------------- >P1;d1khca- ------------------------------305-9175230000545---b---420002004460a657058------------720003010458----221140a--7025--00-5057105-----792176870160034002403610a391a37ab3657208401700397078456504 >P1;d1mhna- --------------------------------48b086728000618---64-7631204046057a-----------------852030406b4b7----7261606--60354-a47---------------------------------------------------------------------- >P1;d1oz2a1 c9657864277594a55699648b7632994a0-9377656000222---966731220202427-------------------c2502030173--67760131603185027---8622984a4814126-b5------85a5-------------------------------------------- >P1;d1oz2a2 --677865266495a5559865b--54784870aa286955000113---566a50020103414-------------------17501010273--78931130439174027---7530a85a3833324-958-----75a8-------------------------------------------- >P1;d1wjra1 -------------------------------44a4077600000207---955820000102518-------------------805020110205b45731242307172035---063077d44712008704542989506720570165085850496018a68ba------------------- >P1;d2g3ra1 -----------------------------------954853030238---85-6835504036537b------------------84120404-777----5330647--10545-5a----------------------------------------------------------------------- >P1;d2hqxa1 --------------68187107702851884---d2a77-300033-75----65110051355459------------------751302000535----624044a--300704---87142607432----------------------------------------------------------- >P1;d2jnga1 ------------------63a5a63a4107802a60656140302673840557240305514------------------c17-540303063366----2260405--104010--884-------------------------------------------------------------------- >P1;d2l89a- ------------------------------999970a3051010338---9--86310000344-236------746a88c7455120203102887----636233b--30550-7572048319-----28893498235005203265a14b5b6389c--------------------------- >P1;d2l8da1 ------------------------------49c35086734020243---b5-a7256060560669-----------------65304050a-976----434052a--20536-796a--------------------------------------------------------------------9 >P1;d3fdra- ---------------91a-21-9017404a4966928764100023786----a20000403554b8------------------73120110053-----643056---500805---9714-91734199--------------------------------------------------------- >P1;d4rxja- -----------------------------------2757230103a------a95333030153805----------a16b647ab0100214a577-----30058b--405448ab47a9178559757a-------------------------------------88886775637765757989 >P1;d6iipa1 ----------------------------------708394200034a---b--533000101827bb39815b------------932101000347----633123a--4025--07743a8217-------728383045016105453a3------------------------------------ Translating the sequences ------------------------------****CCCCC*EEEEE*C---C--**EEEEEE*****************-----**C*EEEEECCCC*----EEEE***--**E**-**********-----*****************************----------------------------- ------------------------------***-CCCCCCEEEEECC---C---*EEEEEEE***********------------CEEEEEECCCC*----EEEE***--**E*--**-*******-----********************************************************** --------------------------------**CCCCCCEEEEECC---C*-C*EEEEEEE*****-----------------*CEEEEEECCCC*----EEEE***--*****-***---------------------------------------------------------------------- *********************************-CCCCCCEEEEE*C---C****EEEEEEE***-------------------*CEEEEEECCC--*****EEE*******E*---***************-**------****-------------------------------------------- --*********************--*********CCCCCCEEEEECC---C**C*EEEEEEE***-------------------*CEEEEEECCC--*****EEE*******E*---***************-***-----****-------------------------------------------- -------------------------------***CCCCCCEEEEECC---C**C*EEEEEEE***-------------------*CEEEEEECCCC*****EEEE*********---*****************************************************------------------- -----------------------------------CCCCCEEEEECC---C*-C*EEEEEEE*****------------------CEEEEEEC-CC*----EEEE***--**E**-**----------------------------------------------------------------------- --------------*****************---CCCCC-*EEEEC-**----C*EEEEEEE*****------------------CEEEEEECCCC*----EEEE***--**E***---***********----------------------------------------------------------- ------------------*****************CCCCCEEEE*CC***C**C*EEEEEEE*------------------***-CEEEEEECCCC*----EEEE***--**E***--***-------------------------------------------------------------------- ------------------------------****CCCCC*EEEEE*C---C--**EEEEEEE**-***------************EEEEEECCCC*----EEEE***--**E**-**********-----*******************************--------------------------- ------------------------------****CCCCCCEEEEECC---C*-C*EEEEEEE*****-----------------*CEEEEEEC-CC*----EEEE***--**E**-****--------------------------------------------------------------------* ---------------***-**-************CCCCCCEEEEECC**----C*EEEEEEE*****------------------C*EEEEECCCC-----*EEE**---**E***---****-********--------------------------------------------------------- -----------------------------------CCCCCEEEEE*------*C*EEEEEE******----------********CEE*EEECCCC*-----**E***--**E*******************-------------------------------------******************** ----------------------------------CCCCCCEEEE*CC---C--C**EEEEE************------------C*EEEEECCCC*----EEEE***--**E*--**********-------********************------------------------------------ 63748.tem _________________________________ -------------------**-*--*********CCCCCCEEEEECC---C**C*EEEEEEE*****-----------------*CEEEEEECCCC*----EEEE***--**E**-****************-********************------------------------------------ Structural block scores 0 18 - 4.5 M 75.0 75.0 75.0 6.7 13.4 75.0 75.0 56.8 71.4 75.0 75.0 64.2 75.0 75.0 19 20 * 3.9 M 75.0 75.0 75.0 7.5 7.0 75.0 75.0 0.5 6.8 75.0 75.0 1.5 75.0 75.0 23 24 - 4.2 M 75.0 75.0 75.0 9.2 75.0 75.0 75.0 1.0 4.5 75.0 75.0 0.5 75.0 75.0 25 33 * 3.4 M 45.4 50.9 59.7 13.2 5.9 52.1 75.0 28.8 4.8 45.7 44.8 5.6 75.0 75.0 34 39 C 4.8 H 4.2 4.5 5.8 6.2 6.8 4.0 17.7 19.2 4.0 4.2 4.8 6.0 16.3 5.2 40 44 E 4.9 H 1.6 1.0 2.8 1.6 1.2 0.4 1.6 1.2 1.8 1.0 1.6 0.6 1.4 1.0 45 46 C 4.5 M 7.2 4.5 4.5 2.0 2.0 3.5 5.5 39.0 6.5 5.5 3.5 5.0 42.8 7.2 47 49 - 4.5 M 75.0 75.0 75.0 75.0 75.0 75.0 75.0 29.0 5.0 75.0 75.0 29.7 75.0 75.0 51 52 * 3.6 M 75.0 75.0 39.5 6.0 6.0 5.0 40.0 75.0 5.0 75.0 40.0 75.0 42.8 75.0 55 61 E 4.9 H 0.4 0.6 2.0 1.3 0.9 0.4 2.9 1.6 2.6 1.0 3.4 1.0 1.9 0.7 62 66 * 1.8 P 4.2 4.9 5.7 32.6 31.8 32.8 6.5 5.6 60.8 17.6 5.4 6.7 4.2 8.0 67 83 - 4.5 M 26.3 50.4 75.0 75.0 75.0 75.0 75.0 75.0 63.0 31.1 75.0 75.0 46.8 50.7 86 91 E 4.9 H 0.8 0.8 1.5 1.7 1.2 1.5 1.8 1.8 1.7 1.3 2.0 1.3 0.7 1.2 92 95 C 4.8 H 3.9 2.5 8.2 21.5 21.8 1.8 23.2 2.0 4.5 4.5 25.4 2.0 6.6 1.8 97 100 - 4.4 M 75.0 75.0 75.0 6.5 6.8 4.8 75.0 75.0 75.0 75.0 75.0 75.0 75.0 75.0 101 104 E 4.7 H 0.5 1.5 4.0 1.2 1.2 2.2 2.8 3.0 2.5 4.2 2.8 3.2 19.5 3.2 105 107 * 1.1 P 5.5 4.8 4.0 3.0 5.3 3.3 5.7 6.2 3.0 5.8 5.8 28.7 8.2 5.2 108 109 - 4.4 M 75.0 75.0 75.0 4.5 4.0 4.0 75.0 75.0 75.0 75.0 75.0 75.0 75.0 75.0 110 111 * 1.0 P 1.0 3.5 3.0 2.5 2.0 1.0 0.5 1.5 0.5 1.5 1.0 2.5 2.0 2.0 113 114 * 1.9 P 1.5 40.0 4.5 41.0 41.0 40.0 4.5 3.5 0.5 2.5 4.5 4.0 4.0 40.0 116 131 * 2.9 P 26.6 30.0 62.3 9.4 9.4 8.6 66.6 26.2 62.2 26.4 58.3 22.8 7.3 31.2 133 152 * 3.7 M 3.9 3.0 75.0 54.8 51.4 4.2 75.0 75.0 75.0 4.3 75.0 75.0 75.0 3.9 153 188 - 4.5 M 61.5 4.7 75.0 75.0 75.0 42.4 75.0 75.0 75.0 58.2 73.2 75.0 37.1 75.0 >>>>>>