Reading input alignment file to find conserved blocks of secondary structure The input structure based alignment from Comparer _____________________________________________ >P1;d1k3ra2 -----------------------------------------------------------------------------------------CCCCEEEEEEECCCCCCCC----------CHHHHHHHHHHHHHHHHHCCCCEEEEEECCCCCCHHHHHHHHHHHHCCHHHHHHHCCCCHHHHHHHHCCCCC------CCCEEEEEEEEHHHHHHHH--CCCEEEEECC--CCCCCCCCHHHHHHHHCCCCEEEEECCCCCCCCCC---CCCC--EEECCCCCCCCCCCCHHHHHHHHHHHHHHHCC---------------------- >P1;d1v2xa- --------------------------------------------------------------------CCIIIIIHHHHHHHHHC----CCCCCEEEEEECCC-------------------CHHHHHHHHHHHHHCCCCEEEEE-------CHHHH---------------------------CCCCCCCCCCHHHCCEEEEEC-CHHHHHHHHHHCCCEEEEECCCCCCEEHHHC--CCCC------CEEEEECCCCCCCCHHHHHHCC--EEEECCCCCCCCCCCHHHHHHHHHHHHHHHHHHCCHHHCCCCCHHHHHHHHHHC >P1;d2v3ka- CCCCCCCCCCCCCCCCCEEEEECCCEEC-------------------CCEECCCCCCHHHHHCCCCHHH-CCHHHHHHHHHHHHCCHHHHCCCCCEEEECCC-----CCEEEECCCCC-CCCCHHHHHHC-CHHHHH--CEEECC-------------------------------------------------CCCCEEEEEECCCHHHCCCC----CEEEEEECC--CCCCC--CHHHHHHCCCCCCEEEEEEEECCCCCC-CCCCCC----CEEECCC-CCC-CCHHHHHHHHHHHHHHHCCC--------------------- >P1;d3aiaa1 --------------CEEEEEECCCCCCCCCCHHHCCC-------------------------------CCCCHHHHHHHHHHHHCCCCCCCCCCEEEEEECCCCCCCEEEEEECCCCCCCCCCHHHHHHHHHHHHHHHHHCC----------CCHHH---------------------------CCEEEEC------CEEEECC--CHHHHHHHHHHCCCEEEEECC--CCEEHHHC--CC-C------CEEEEEECCC-CCCHHHHHHHHHCCCEEEECC-CCC-CCHHHHHHHHHHHHHHC------------------------ >P1;d3bbda1 -------------CEEEEEEEECCCCCCHHHHHH--CCCCCCCC----CCCCCHHHHCCC-CCCCCCC-CCCHHHHHHHHHHHHCCHHHHCCCEEEEEEECC-----CEEEEECCCCC-CCCCHHHHHHC-CCCCCC--CCC--------------------------------------------------------CCEE-EECCHHHHHHHC---CCCEEEEEE--EEEEC--CHHHHHH-----CCEEEEECCCCCCCCCCHHHCC--CEEEEEECC-CCC-C-CHHHHHHHHHHHHC------------------------- >P1;d3o7ba- ------------CCEEEEEEEECCCCCCHHHCCCHHHHHHHCCCCCHHHCCCCHHHHHHHCCCCCCHHHCCCCHHHHHHHHHHHCCC---CCCEEEEEEECC-----CCEEEECCCCC-CCCCHHHHHHHHHHHHHH--CEEEEC---------------------------------------------------CEEEEEEECCCHHHHCC-----CCEEEEECC--CCCCC--CHHHHCC----CCEEEEEECCCCCCCCHHHHHHH--CCEEEECCC-CCC-CCHHHHHHHHHHHHHHHHC---------------------- PSA >P1;d1k3ra2 -----------------------------------------------------------------------------------------196040000000000561b----------6356104100400300151806200005087b040700310041021487425750758940430a401809------5505031267505400860--7040100125--a144077349504840391820000010244804b---0b04--0401032c1a8a41500620540052047009---------------------- >P1;d1v2xa- --------------------------------------------------------------------85973676578126305----40022000001307-------------------53400020051035010120001-------50075---------------------------92528420d103730404307-6054007204759030001156970440570--6026------40000000187605b6028204--510213199a79335115203400410251056431086320789317701760 >P1;d2v3ka- bb93940307449420000000203147-------------------64300129616a3078c47236-03051006000300415006334000001075-----94001020607-00673970192-160147--71161a-------------------------------------------------a767420421a540372009----403200005--80832--6017106906b710000003027a926-205610----9430001-a96-170351054007001602a1--------------------- >P1;d3aiaa1 --------------11000102701011906194058-------------------------------70330000030013001499721770200000318542200010103507904573630030045005303507----------67516---------------------------7216025------0010120--304800540395915000033--81460770--90-7------6100001177-509960271058290430102-888-25006206400611475------------------------ >P1;d3bbda1 -------------5210000300002018704b4--09669807----240005730770-6808546-003020004002300704006555030000024-----42015052709-02772470044-160049--693--------------------------------------------------------8306-882501500461---706600026--50951--7266047-----130000001287408059860a--191640006-985-2-04420130051009------------------------- >P1;d3o7ba- ------------67000000000002017503a372077219394624200002940660077083250003021005001400507---145040000005-----53002020609-036737800520050055--54126c---------------------------------------------------b6120203b45074008-----a07000025--70694--7157008----a3000001001769038701710--aa2420105-a78-2914510540061027215---------------------- Translating the sequences -----------------------------------------------------------------------------------------*CCC*EEEEEECC*****C----------*****HHHHHHHHHHHHH***CEEE***********************************************------*C*EEEEE***HHHHHHH*--*CCEEEEECC--CC**C**CHHHH*******C*EEEE*CCCCCCCC*---**C*--*EE**CCC*CCC*CCHHHHHHHHHHHHHHH**---------------------- --------------------------------------------------------------------*C*****HHHHHHHHHC----*CCC*EEEEEECC*-------------------CHHHHHHHHHHHHH***CEEE**-------*****---------------------------*************C*EEEEE*-CHHHHHHH****CCEEEEECC**CC*****C--****------*EEEEECCCCCCCC**HHH*C*--*EEE*CCC*CCC*CCHHHHHHHHHHHHHHH************************ *****************EEEE*CCC**C-------------------**********************-CC*HHHHHHHHHHHCC****CCC**EEEE*CC-----C*EEEECCCCC-CCCCHHHHHH*-*HHHH*--CEEE**-------------------------------------------------***C*EEEEE**CHHH****----C*EEEEECC--CC**C--CHHHH*******C*EEEEE**CCCCCC-*****C----*EEECCC-CCC-CCHHHHHHHHHHHHHHH***--------------------- --------------***EEEE*CCC**C*********-------------------------------*CCC*HHHHHHHHHHHCC****CCC*EEEEEECC*******EEEECCCCC*CCCCHHHHHHHHHHHHH******----------*****---------------------------*******------C*EEE**--CHHHHHHH****CCEEEEECC--CC*****C--**-*------*EEEEE*CCC-CCC**HHH*******EEE*CC-CCC-CCHHHHHHHHHHHHHH*------------------------ -------------****EEEE*CCC**C******--********----************-*******-CCC*HHHHHHHHHHHCC****CCC*EEEEEECC-----C*EEEECCCCC-CCCCHHHHHH*-******--C**--------------------------------------------------------**EE-E**CHHHHHHH*---CC*EEEE**--****C--CHHHH**-----C*EEEEECCCCCCCC**HHH*C--**EEEE*CC-CCC-C-*HHHHHHHHHHHH*------------------------- ------------*****EEEE*CCC**C*****************************************CCC*HHHHHHHHHHHCC*---CCC*EEEEEECC-----C*EEEECCCCC-CCCCHHHHHHHHHHHHH*--CEEE**---------------------------------------------------***EEEEE**CHHHH**-----CCEEEEECC--CC**C--CHHHH**----*C*EEEEECCCCCCCC**HHH**--**EEEECCC-CCC-CCHHHHHHHHHHHHHHH**---------------------- 75217-1.tem _________________________________ -------------****EEEE*CCC**C******--*-----------************-********CCC*HHHHHHHHHHHCC****CCC*EEEEEECC*----C*EEEECCCCC-CCCCHHHHHHHHHHHHH***CEEE**-------*****---------------------------******------*C*EEEEE**CHHHHHHH*--*CCEEEEECC--CC**C**CHHHH**----*C*EEEEECCCCCCCC**HHH*C*-**EEEECCC-CCC-CCHHHHHHHHHHHHHHH**---------------------- Structural block scores 0 12 - 4.5 M 75.0 75.0 5.8 75.0 75.0 69.7 13 16 * 2.9 P 75.0 75.0 1.5 19.2 2.0 1.8 17 20 E 4.3 M 75.0 75.0 0.0 0.2 0.8 0.0 22 24 C 4.3 M 75.0 75.0 1.7 2.7 0.0 0.0 25 26 * 2.7 P 75.0 75.0 2.5 0.5 1.0 1.0 28 33 * 3.4 M 75.0 75.0 75.0 4.8 5.8 4.8 34 35 - 4.1 M 75.0 75.0 75.0 2.5 75.0 4.5 37 47 - 4.2 M 75.0 75.0 68.7 75.0 31.4 4.9 48 59 * 3.4 M 75.0 75.0 3.8 75.0 2.9 2.4 61 68 * 3.3 M 75.0 66.6 6.2 66.5 14.0 4.0 69 71 C 4.2 M 75.0 7.0 26.0 2.0 1.0 1.0 73 83 H 4.4 M 75.0 4.6 1.4 0.6 1.0 1.2 84 85 C 4.4 M 75.0 40.0 2.5 2.5 3.5 2.5 86 89 * 2.9 P 56.5 57.2 2.8 6.8 2.5 58.0 90 92 C 5.0 H 5.0 0.7 3.3 5.0 5.0 3.3 94 99 E 4.8 H 0.0 0.2 0.2 0.3 0.5 0.7 100 101 C 5.0 H 0.0 1.5 6.0 2.0 3.0 2.5 103 106 - 4.1 M 3.0 75.0 75.0 3.2 75.0 75.0 109 112 E 4.3 M 75.0 75.0 0.2 0.5 1.5 0.5 113 117 C 4.3 M 75.0 75.0 3.0 3.0 4.6 3.4 119 122 C 4.3 M 3.8 57.5 3.2 4.0 4.0 4.0 123 135 H 4.7 H 1.4 1.8 9.1 2.2 8.2 2.7 136 138 * 2.6 P 3.0 0.3 52.3 2.0 53.0 51.7 140 142 E 4.2 M 0.7 0.7 2.7 27.3 29.0 2.3 143 144 * 2.7 P 0.0 0.5 5.8 75.0 75.0 9.2 145 151 - 4.5 M 5.1 75.0 75.0 75.0 75.0 75.0 152 156 * 3.4 M 2.0 3.4 75.0 5.0 75.0 75.0 157 183 - 4.5 M 3.8 75.0 75.0 75.0 75.0 75.0 184 189 * 3.4 M 3.7 5.0 75.0 3.0 75.0 75.0 190 195 - 4.3 M 75.0 3.2 52.9 63.3 75.0 75.0 199 203 E 4.6 H 2.2 2.2 1.8 0.8 18.4 1.4 204 205 * 2.3 P 6.5 41.0 7.8 75.0 5.0 7.8 207 213 H 4.6 H 3.3 2.6 3.0 3.0 2.3 13.4 215 216 - 4.1 M 75.0 5.5 75.0 6.0 75.0 75.0 218 219 C 4.8 H 2.0 4.5 2.0 5.0 3.5 5.2 220 224 E 4.9 H 0.4 0.8 1.0 1.0 2.4 1.4 225 226 C 4.5 M 3.5 3.0 2.5 3.0 4.0 3.5 227 228 - 4.5 M 75.0 7.5 75.0 75.0 75.0 75.0 229 230 C 4.5 M 5.8 3.5 4.0 4.5 2.5 3.5 231 232 * 1.0 P 4.0 4.0 5.5 5.0 7.0 7.5 234 235 * 3.4 M 7.0 6.0 75.0 7.0 75.0 75.0 237 240 H 4.2 M 4.5 39.0 2.2 39.8 3.5 3.2 241 242 * 1.4 P 6.0 4.0 3.0 41.0 5.5 4.0 243 246 - 4.1 M 4.0 75.0 6.6 75.0 75.0 75.0 250 254 E 4.9 H 0.0 0.0 0.0 0.2 0.0 0.2 255 262 C 4.8 H 2.9 3.4 4.9 13.1 3.8 3.2 263 264 * 1.9 P 43.2 8.8 38.5 7.5 2.5 7.5 265 267 H 4.2 M 50.0 3.3 3.7 3.0 7.7 2.7 272 273 * 2.6 P 37.5 40.0 75.0 5.5 5.0 10.5 274 277 E 4.4 M 1.2 1.0 4.0 1.8 2.8 2.0 278 280 C 4.7 H 5.8 4.3 0.3 1.0 2.0 2.0 282 284 C 5.0 H 9.7 8.8 8.5 8.0 7.3 8.5 286 287 C 4.8 H 3.0 4.0 4.0 3.5 38.5 5.5 288 302 H 4.9 H 2.3 1.9 2.1 2.8 6.9 2.5 303 304 * 2.7 P 4.5 2.5 6.2 75.0 75.0 3.0 305 326 - 4.5 M 75.0 4.0 71.6 75.0 75.0 75.0 >>>>>>