Reading input alignment file to find conserved blocks of secondary structure The input structure based alignment from Comparer _____________________________________________ >P1;d1amxa- ------------------------------------------------------------------------C-----CCCCEEEEEE-----CCC--------CCCCEEEEEEEE-CCCCCCCCCCEEEEEEECCCEEEEE---EEEEEEEEE-CCCEEECCCCHHHHHHHHCCCCEEEEE-CCCCEEEEEE-CHHHHC-CE-EEEEEEEEEECC--CC-----CCEEEEEEEEEECCCCCCCEEEEECCEEEEC-- >P1;d1n12a- -------------------------------------------CCCCCCCCCCCCCCCCC--HHHCCC----------C-CEEEEEEEECCCCCCC---------C---CCEEEECCCEE------CCEEECCCCC-----CCCCCEEEEEEEEEE--------CC-------EEEEECCCCC----CCCCCCEECCC--CCCEEEEEEEEEEE-CC----CCCCCCCCCCCCEEEECCC------------------ >P1;d1n67a1 ------------------------------------------------------------------------CCCCHHHCEEEEEEEE-CCCEECHHH--------CCCEEEEEEEECCCCCCCCCEEEECCC--CCEEECCCCCCCCCCCEEEC-----------------CEEEEEEEEC--CCCCEEEEECCHHHHCCCCEEEEEEEEEECCCCCCC-----CEEEEEEEEEC----------CEEEEEEEEECC >P1;d1p5ub- ------------------------------CCCCCCCCCCCCCCCCCCCEEEEEECCCCCCC-----C-------CCCCCCCEEEEEEEECCC------CCCCHHH-----EEEECC---C---CCCCCEEEECCC-----CCC-CEEEEEEEEEC--------CC-------CEECCEECCCCCCCCCCCCC---------CEEEEEEEEEECC-----CCCCCCC-CCCCCEEEECCC------------------ >P1;d1pdkb- ----------------------------CC----------CCCCEECCCCCCCCCC--CC--HHHHHC-------CCCC-CCCCEEEEEEEECCCC----CCHHHH---EEEEEECCEEC----CEEEEECCCC-------CCCCC-EEEEEECCC--------C----------CCCCCCCC----CCCCCCCCC-----CEEEEEEEEEEEC-HHHHHCCCCCCCCCCCCCEEEEEEC------------------ >P1;d1ut1a- ---------------------------------------CEEEEEE---EEEEEEEEEECCCCCCCCCCCCEEEHHHCCCCCEEEEEEEECC---------CCCCC--EEEEEEC------HHHEECCEEEEEEC---------CCCCEEEEEEEEC-----C-----------CCCEEEE----CCEEEECCCCCC------EEEEEEEECC------CCCCCCCEEEEEEEEEEEEEC------------------ >P1;d2axwa1 ---------------------------------------------C---EEEEEECCC-C--------CCCCC------CCCEEEEEEEECC----------CCCC--EEEEEECC-EECCCCCC---EEEEEEC---------CCCCEEEEEEE-C-----C----------CC-EECCC----CCCCCEEEECCCC-----EEEEEEEECC-------CCCCCCCCEECCEEEEEECCCC---------------- >P1;d2cnza- --------------------------------------------CC---EEEEEECCCCC--------CEECC------CCCEEEEEEEECC-----------CCC--EEEEEEECCEECCCCCC---EEEEECC---------CCCCEEEEEEC-H-----HHHH-------CCCEEEEE----CCEEEEEEEC--------CEEEEEEECC------CCCEECCCCCCCEEEEEEECC------------------ >P1;d2okma- ------------------------------------------------------------------------C-----CCCCEEEEEE-----CCC----------CCEEEEEEEE-CCCCCCCCCCEEEEEC-CCCEEECC---CCCEEEEECCCCEEEEE----HHHHHHCC-CEEEEEC--CCCCEEEEE-CHHHHC-CC-EEEEEEEEEECHHHHC-----CCEEEEEEEEEECCC--CCEE-EEEEEEEEC-- >P1;d2uy6b1 -------CCCCCCCCCCCCCEEECCC------------------------CCCCCCCCCCCHHHH-------------CCCCCCEEEEEEEECCC------CCCCC--CCCCEEECCEEC----CEEEEEECCC----------CCCEEEEEECC--------------------CCCCCEEE----ECCCCCC-------CCEEEEEEEEEECC----CCCCCCCCCCCCCCEEECCCC------------------ >P1;d2xg5b- --------CCCCCCCCCCCCEEECCC------------------------CCCCCCCCCC-CCCC-------------CCCCCC-EEEEEEECCCCCCCCCCCCCC--CEEEEEECCCC------CCCCCCCC-----------CCCEEEEEEECC-------------------CCCCCCCC----CCCCCCC-------CCEEEEEEEEEEC--------CCCCCCC-CCCEEEEEEC------------------ >P1;d3jwne- CCCCCCCCCCC----CCCCEEEEEC---------------------------CCCCCCCCHHHHCCCC-------CCCCCCCCCEEEEEEEEEECCCC-C--------EEEEEEECCCC-C---CCCCCEECC-CC-----CCCCCCEEEEEECCC-------------------CCCCCCCCCCCCCCEEECCC--C--CCEEEEEEEEEEECC------CCCCCCCCCCCCEEEEEEC------------------ >P1;d3rkpa2 -------------------------------------------------------------------------------CCCEEEEECCCCCEEEC--------CCCCCEEEEEEEECCCCHHHCCEEEEEEECCCCEEEC----CCCEEEECC----EECCC-----------CCEEEEEE---CCEEEEEECCHHHHC-CCCEEEEEEEEEECCCCCC-----CCCEEECCEEEEECCCCCEEEEECCCEEEEC-- >P1;d4xo9a2 ----------------------------------------CCEEECC--CCCCCCCC-------------------CCCCCEE-CCCEEEECC-----CE--------EEEEEEECCCCCC---CC-CCCCCCCC------CCCCCCEEEEEEEC--------------------CEECCCC----CCEEEEEEC--C--CCEECCEEEEEEECC------CCCCCCCCCCCCEEEEEEC------------------ >P1;d5ihwa1 -------------------------------------------------------------------------CCCHHHEEEEEEEEE----EEEHHHC-HHHCCCCEEEEEEEEEEECCCCCCCCEEEEECC--CCEECCCCCCCCCCCCEECC----------------CCCEEEEEEEE-CCCCEEEEEECCHHHHCCCEEEEEEEEEEECCCCCCC-----CEEEEEEEEEC----------CEEEEEEEEECC >P1;d5lp9a- -----------CCCCEEEEEEEEEECCCCC----------CCCEECCCCCEEEEECCEEE--HHHCCC---------CCCEEEEEEEEEEEEEECCCCCC--------EEEEEEECCCCCC---CCCCCCCCCCCC-----CCCCEEEEEEEECCC-------------------CCCCCCC--CCCCCCCEECC--C--EEEEEEEEEEEEEEE-------EEECEEEEEEEEEEEEEE------------------ >P1;d6swhb- C--CCCCCCCC----CCCCCEEEECC--------------------HHH---CCCCCCCC--HHHCC--------CC-CCCCCCEEEEEEEECCCHHHHC--------CCEEEEECCEE-C---CEEEEECCC-CC-----CCCCCCEEEEEEECC-------------------CCCCCCCCC---CCCCCCC-------CCEEEEEEEEEECC------CCCCCCCCCCCCEEEEECC------------------ PSA >P1;d1amxa- ------------------------------------------------------------------------c-----a460050305-----038--------837420202020-025434033503050305b104042---530206043-6568514a860264027405a060705-5a72204040-238300-60-203010204057--6a-----365030402030417b6a4263652433066-- >P1;d1n12a- -------------------------------------------4660827c481719b08--495045----------a-0434351507605338---------8---7402050a534------8400105a00-----65a810001201108--------84-------933a506145----514064366b9--27131100020022-59----930587a292917172317------------------ >P1;d1n67a1 ------------------------------------------------------------------------76601a5078180408-1aa204188--------953050502010268066502030601--820400477ba29034041c-----------------9740070843--b77103040272058569180805030201692078-----43815040004----------b35263504042 >P1;d1p5ub- ------------------------------bbaa9a7a898898755727374882992935-----9-------660665341010301508------6702031-----03030b---4---555320013075-----b77-34020101053--------b9-------94000300663247536077---------a40503030350b-----b5a0589-151a27160848------------------ >P1;d1pdkb- ----------------------------99----------9640320a05a38181--06--066103-------5770-3083361303033079----a31a83---0300054850a----4170104089-------70443-000001002--------8----------85205056----409b9418e-----1030301010100-670275340576a181a27141638------------------ >P1;d1ut1a- ---------------------------------------0804667---a4631703025992849ba987012385066716046181619---------b2995--2000306------96017875000117---------7583303060605-----6-----------c270425----900011475521------1550102049------623a04376030102402067------------------ >P1;d2axwa1 ---------------------------------------------3---5243794aa-7--------c8608------5334003030108----------7a06--00201061-7316c510---3000605---------76845040202-4-----a----------90-6539b----b914004284967-----5050101017-------628229760615010406158b---------------- >P1;d2cnza- --------------------------------------------a1---8352674ac49--------36718------652600402050a-----------737--10002042c52449200---3030506---------83764010001-6-----8037-------41353366----a863110070--------6440100038------922814806151605031375------------------ >P1;d2okma- ------------------------------------------------------------------------9-----a360030604-----26b----------a640401000-0154510343030500-59005033---a30600031a7653615----29503937-0070714--682405050-438504-60-0020402050499047-----3a3040603050326--7634-478325091-- >P1;d2uy6b1 -------976899898a56053515b------------------------8462907a26a7048-------------83408527130403918------4058c--58002041720c----a424004086----------c0600010616--------------------94130455----848110e-------65205040203313----5bc1706ba18092714093b------------------ >P1;d2xg5b- --------88a6c9775460622159------------------------8562916013-4068-------------881046-3150405809058e4010133--60400043925------57310509-----------802000102037-------------------74205257----5052182-------8220503040143--------70958c0-2a18041537------------------ >P1;d3jwne- cab7898a87a----7694072855---------------------------a1a1a29684179078-------88702508336050402803960-5--------10111045a30-9---459400205-b5-----b60060000010469-------------------57215041769529438064--3--751315030102005------3707637080a27160548------------------ >P1;d3rkpa2 -------------------------------------------------------------------------------70506020468456261--------935540200030501b405506501010603a40402----c70403038----76187-----------90050639---c35020305317605-b48401030402057b179-----8360501030301247778343507402020-- >P1;d4xo9a2 ----------------------------------------c405054--7a292a05-------------------b476327-070405088-----73--------800020458022b---96-00030608------9830800001012b--------------------9950307----72150a504--7--a44606030202619------ba25b48070907151456------------------ >P1;d5ihwa1 -------------------------------------------------------------------------b41292050760506----3150660-a8843b940010203030378076602010301--74032228578981630419----------------87630060816-7862304050261046588070502020111694059-----55426030000----------846355608073 >P1;d5lp9a- -----------b2981050530305173a6----------8006029a025130807616--184026---------5532333360704039052a406--------3000006392159---946300209468-----bc1045000000045-------------------5800305--06420332808--9--750404050201014-------705214060606040509------------------ >P1;d6swhb- c--b7798a9a----96660626074--------------------a95---7291aa07--2a507--------76-6521752712030470587204--------50201040920-b---538300109-a6-----ab2062000000047-------------------382120558---4572606-------84105020102002------8704357090a18140729------------------ Translating the sequences ------------------------------------------------------------------------*-----CCCCE*EEEE-----***--------*****EEEEEE*-***C***C***EE****C*******---***EEEEE*-********************C******-***C******-C*****-C*-EEEEEEEEE***--**-----CC******EEEE**C****************-- -------------------------------------------*****************--******----------C-C*E*EEEEE*******---------*---**EEEE*****------**EE****C*-----***CC**EEEEE***--------**-------**********----***********--*C*EEEEEEEEEE*-**----****CC******EEEE**C------------------ ------------------------------------------------------------------------*******C**E*EEEE-*********--------***EEEEEE*****C***C***EE***--*********CCC****EE**-----------------**********--**C*******C******C*EEEEEEEEEE*******-----C*******EE*----------************ ------------------------------********************************-----*-------***CCCCE*EEEEE****------*******-----EEEE**---C---C****E****C*-----***-C**EEEEE***--------**-------*************C******---------*EEEEEEEEEE**-----*****CC-*****EEEE**C------------------ ----------------------------**----------****************--**--******-------***C-CC**EEEEE*******----******---EEEEEE*****----C***EE****-------***CC-*EEEEE***--------*----------C*******----*******C*-----C*EEEEEEEEEE*-**********CC******EEEE**C------------------ ---------------------------------------*******---*****************************CCCCE*EEEEE***---------*****--*EEEEE*------*******EE****C---------CCC*EEEEE****-----*-----------*C*****----*C*******C**------EEEEEEEE**------******C*******EEEE**C------------------ ---------------------------------------------*---*********-*--------*****------CCCE*EEEEE***----------****--*EEEEE**-***C***C---EE****C---------CCC*EEEEE**-*-----*----------**-*****----*C*******C***-----EEEEEEEE**-------*****CC******EEEE**C**---------------- --------------------------------------------**---***********--------*****------CCCE*EEEEE***-----------***--*EEEEEE*****C***C---EE****C---------CCC*EEEEE**-*-----****-------**C*****----*C*******C--------*EEEEEEE**------******CC******EEEE**C------------------ ------------------------------------------------------------------------*-----CCCCE*EEEE-----***----------***EEEEEE*-***C***C***EE***-C*******---CC*EEEEE*********----********-C******--**C******-C*****-C*-EEEEEEEEE*******-----CC******EEEE**C--****-*********-- -------*******************------------------------***************-------------CCCC**EEEEE******------*****--****EEE*****----C***EE****----------CCC*EEEEE**--------------------C*******----*******-------C*EEEEEEEEEE**----******CC******EEE***C------------------ --------******************------------------------**********-****-------------CCCC**-EEEE*****************--*EEEEEE****------********-----------CCC*EEEEE***-------------------C*******----*******-------C*EEEEEEEEEE*--------***CC**-***EEEE**C------------------ ***********----**********---------------------------****************-------***CCCC**EEEEE*********-*--------*EEEEEE****-C---C****E***-C*-----***CCC*EEEEE***-------------------C**********C*******C--*--*C*EEEEEEEEEE**------****CC******EEEE**C------------------ -------------------------------------------------------------------------------CCCE*EEE*********--------*****EEEEEE*****C***C***EE****C******----CC*EEEE**----*****-----------*C******---*C*******C*****-C**EEEEEEEEE*******-----CC******EEEE**C****************-- ----------------------------------------*******--********-------------------**CCC*E-***EE****-----**--------*EEEEEE*****C---C*-*******C------***CCC*EEEEE**--------------------C******----C*******C--*--*C*E**EEEEEEE**------****CC******EEEE**C------------------ -------------------------------------------------------------------------*********E*EEEE----*******-*********EEEEEE*****C***C***EE***--*********CCC****EE**----------------***********-***C*******C******C*EEEEEEEEEE*******-----C*******EE*----------************ -----------*******************----------********************--******---------*CC**E*EEEEE***********--------*EEEEEE*****C---C*********C*-----***C***EEEEE***-------------------C******--**C*******C--*--***EEEEEEEEEE**-------***C*******EEEE***------------------ *--********----***********--------------------***---********--*****--------**-CCCC**EEEEE***********--------**EEEEE****-C---C***EE***-C*-----***CCC*EEEEE***-------------------C********---*******-------C*EEEEEEEEEE**------****CC******EEEE**C------------------ 49401-1.tem _________________________________ -------------------------------------------****--***********--******----*--***CCCCE*EEEEE*********-*-*****--*EEEEEE*****C***C***EE****C*-----***CCC*EEEEE***-----------------**C*******-**C*******C***--*C*EEEEEEEEEE****-*******CC******EEEE**C------------------ Structural block scores 0 42 - 4.5 M 75.0 75.0 75.0 55.2 67.1 68.3 75.0 75.0 75.0 44.8 46.1 42.0 75.0 70.2 75.0 38.7 43.3 43 46 * 3.8 M 75.0 4.0 75.0 6.2 1.2 23.5 57.0 40.4 75.0 75.0 75.0 75.0 75.0 3.5 75.0 4.2 58.9 47 48 - 4.2 M 75.0 5.0 75.0 4.5 5.2 75.0 75.0 75.0 75.0 75.0 75.0 75.0 75.0 75.0 75.0 5.2 7.0 49 59 * 2.8 P 75.0 6.3 75.0 6.2 17.5 3.8 12.5 6.5 75.0 11.8 10.5 25.0 75.0 24.6 75.0 3.5 24.7 60 61 - 4.2 M 75.0 75.0 75.0 4.0 75.0 9.0 75.0 75.0 75.0 8.8 39.5 6.0 75.0 75.0 75.0 75.0 75.0 62 67 * 3.7 M 75.0 4.5 75.0 64.0 2.7 7.5 75.0 75.0 75.0 39.5 39.8 5.3 75.0 75.0 75.0 3.5 16.6 68 71 - 4.5 M 75.0 75.0 75.0 75.0 75.0 6.0 6.6 4.2 75.0 75.0 75.0 75.0 75.0 75.0 75.0 75.0 75.0 73 74 - 4.5 M 75.0 75.0 6.0 75.0 75.0 2.5 75.0 75.0 75.0 75.0 75.0 75.0 75.0 75.0 7.8 75.0 75.0 75 77 * 3.6 M 75.0 75.0 3.8 4.0 6.3 4.3 75.0 75.0 75.0 75.0 75.0 7.7 75.0 30.2 4.0 51.7 29.3 78 81 C 4.4 M 5.1 22.4 5.0 5.0 19.5 5.0 21.5 22.0 4.9 3.8 4.2 1.8 21.8 4.5 1.8 3.2 3.5 84 88 E 4.8 H 16.6 2.8 17.4 0.8 2.6 4.0 1.2 1.2 17.0 2.6 16.8 2.8 2.4 2.2 17.2 3.2 2.4 89 97 * 2.6 P 51.2 20.2 5.0 43.2 19.4 51.8 51.0 51.7 52.2 27.8 4.3 3.6 20.2 44.0 27.3 4.2 4.0 101 105 * 3.4 M 47.2 61.6 75.0 1.2 5.1 7.3 19.7 33.4 75.0 5.9 1.6 75.0 47.4 75.0 6.9 75.0 75.0 106 107 - 4.2 M 5.5 75.0 7.0 75.0 75.0 75.0 75.0 75.0 8.2 75.0 75.0 75.0 5.0 75.0 6.5 75.0 75.0 109 114 E 4.8 H 1.0 3.0 2.0 26.0 1.3 1.5 1.5 1.0 0.8 2.3 1.3 1.2 0.8 1.0 1.0 1.0 1.2 115 119 * 1.8 P 16.4 4.5 1.8 47.3 5.5 75.0 17.4 5.1 16.2 4.5 18.8 18.7 3.5 3.4 2.6 4.0 17.2 121 123 * 3.5 M 2.3 75.0 4.0 75.0 75.0 5.0 6.2 3.7 2.0 75.0 75.0 75.0 3.3 75.0 4.3 75.0 75.0 125 127 * 1.8 P 2.7 29.0 0.7 4.3 2.7 7.3 75.0 75.0 2.3 3.3 5.0 6.0 3.7 27.0 0.7 4.3 4.7 128 129 E 4.3 M 1.5 0.0 1.5 1.0 0.5 2.5 1.5 1.5 1.5 0.0 0.5 0.0 0.5 0.0 0.5 0.0 0.0 130 133 * 1.4 P 2.0 4.1 20.5 1.0 5.2 0.5 1.5 2.0 20.0 4.5 22.2 20.5 1.8 2.2 19.8 3.8 21.2 136 140 - 4.2 M 1.8 75.0 1.2 75.0 75.0 75.0 75.0 75.0 1.6 75.0 75.0 75.0 2.0 75.0 2.2 75.0 75.0 141 143 * 3.1 M 50.7 7.2 6.0 8.5 3.7 75.0 75.0 75.0 51.0 75.0 75.0 5.8 75.0 6.7 5.0 8.3 8.0 144 146 C 4.5 M 27.7 3.0 8.0 27.3 27.3 6.7 7.0 6.0 29.5 6.2 3.3 2.0 31.5 2.7 8.0 3.0 2.7 148 152 E 4.8 H 2.4 0.8 2.2 0.8 0.2 2.4 2.2 1.0 1.8 1.4 0.6 0.2 2.0 0.4 2.8 0.0 0.0 153 155 * 1.9 P 28.0 3.0 29.5 2.7 0.7 2.0 25.7 25.3 6.2 27.3 3.3 6.3 52.7 29.5 28.3 3.0 3.7 156 172 - 4.5 M 4.6 66.9 71.1 67.4 71.1 66.8 67.0 54.4 21.0 75.0 75.0 75.0 54.6 75.0 67.1 75.0 75.0 173 174 * 3.4 M 2.5 6.0 5.5 6.5 75.0 43.8 4.5 2.5 41.0 75.0 75.0 75.0 42.0 75.0 4.5 75.0 75.0 176 182 * 1.5 P 13.3 4.5 13.9 2.1 3.3 24.0 26.4 24.7 13.4 3.1 3.6 2.9 14.0 14.1 13.7 13.0 3.3 184 185 * 3.2 M 8.8 75.0 9.2 3.0 75.0 42.0 43.2 42.8 7.0 75.0 75.0 7.5 43.8 75.0 7.0 3.0 75.0 187 193 * 1.1 P 12.1 3.3 1.4 14.7 5.5 2.6 2.7 2.6 12.7 5.2 3.3 4.6 2.1 3.4 2.0 2.6 4.3 195 197 * 3.3 M 4.7 8.8 2.3 75.0 54.8 26.0 7.3 75.0 5.3 75.0 75.0 51.0 4.7 52.3 1.7 53.0 75.0 198 199 - 4.2 M 0.0 75.0 6.5 75.0 75.0 75.0 75.0 75.0 2.0 75.0 75.0 75.0 2.5 75.0 5.5 75.0 75.0 203 212 E 4.8 H 8.7 0.9 2.6 2.3 0.9 2.7 2.0 2.6 8.8 1.9 1.9 1.5 2.2 2.5 1.8 1.6 1.1 213 216 * 3.1 M 21.8 22.8 4.5 40.4 22.0 75.0 75.0 75.0 5.5 38.5 57.0 38.8 5.9 40.0 5.0 38.8 38.0 218 224 * 3.1 M 55.9 34.6 55.7 26.0 3.7 14.4 24.3 14.4 55.1 16.0 45.1 34.6 55.9 36.3 55.6 44.6 34.9 225 226 C 4.7 H 4.5 7.5 3.5 8.5 6.5 5.0 8.0 4.0 6.8 8.8 6.5 4.5 5.5 7.8 5.0 1.5 4.0 227 232 * 1.1 P 2.0 5.6 3.0 15.8 5.5 1.7 3.0 3.2 2.2 5.1 16.8 4.6 2.0 4.0 2.5 2.7 4.6 233 236 E 4.8 H 1.2 4.2 19.8 3.5 3.2 2.0 1.2 2.2 2.0 3.0 3.2 3.5 1.5 3.5 18.8 2.5 3.2 237 238 * 1.6 P 2.5 2.0 75.0 6.0 4.5 3.0 3.5 5.0 2.5 6.0 4.0 4.5 1.5 4.5 75.0 2.5 4.5 240 257 - 4.4 M 12.7 75.0 27.5 75.0 75.0 75.0 67.8 75.0 24.1 75.0 75.0 75.0 11.6 75.0 28.1 75.0 75.0 >>>>>>