Reading input alignment file to find conserved blocks of secondary structure The input structure based alignment from Comparer _____________________________________________ >P1;d1v9ta- -------------CCCCEEEEEEC-----CEEEEEEECCCCCHHHHHHHHHHHH-----------C----CCCCCCCEEEEECCCEEEECCCCC-CCCCCCC----------------------------CCCCCCHHH-CCCC-CCCEEEECCCCCCCCCCCCEEEECCCCHHHCCCCCCCCCCEEEEEEE--CHHHHHHHHCCCEEEECCEEEEECCCCCEEEEEECC----- >P1;d1w74a- -------------CCCCEEEEEEC-----CEEEEEEECCCCCHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCEEEEEEECCCEEEECCC-CCCCCC--CCCC--------------------------CCCCCCCC-CCCCCCCCEEEECCC-CCCCCCCCEEEECCCCHHHCC-----CCCEEEEECCHHHHHHHHHHHCCCCC----CCCCCCCCCEEEEEEEE------ >P1;d1x7fa1 -----------------------------CEEEEEEECC-------CCC---------------HHHHHHHHCCCEECCCCCCCCEEEECCHHHHHCCCCCCCCC-----------------------------------CC-CCCCCEEEEECHHHHHH-CCCEEEECCC------CCCCCCEEEEEEEC-HHHHH----HHHHCCC-----------CCEEEEEC-------- >P1;d1zx8a1 -----------------CEEEECC-----CCEEEECCCCC--CHHHHHHHH---------------------HCCEEEECEECCCEEEEECCCCCCCCCEE----CCCC-------------------------------------CCCEEEEHHH------CEEEEECCCCCC-CCCCCCCCCEEEEECCC----CCCCCCC---------------CCCEEEEEECC-----C >P1;d2b71a1 CHHHHHHHHHHHHHHCCEEEEEEC-----CEEEEEEECCCCCHHHHHHHHHHHH---------C------CCCCCEEEEEEECCCEEEECCC-CCCCCCCCCCCC-------------------------CCCCCCCCC-CCCCCCCCEEEECCC-CCCCCCCCEEEECCCCHHHCC-----CCCEEEEEEE--CHHHHHHHHCCCCC----CCCCCCCCCEEEEEEC------- >P1;d2mvza- --------------CEEEEEEEECC----CCEEEEEECCCCCHHHHHHHHHHHCC---------------CCCCCCCCCCCCCCCEEECCCCCC-----------------------------CCCCCCCCCCCCCCCCCCCCC-CCCEEEECCC-CCCCCCCCEEEECCCCCCCCC-----CCEEEEEEEE--CHHHHCCCC---------------CCCCEEEEEEEEEC--- >P1;d2phcb1 ------------------------------CEEEEEECCCCCCCHHHHHHHH--------CCCHHHHHHHHCC-CEEEEEEECCCEEEEECCCHHH---CCCCCC-----------------------------------CEEEECCCEEEEEC--------CEEEEECCC------EEEC--CEEEEECC-CCCCCCCCCCCCCCCC-----------CCEEEEEEE---CCCC >P1;d2wfia- -------------CC-CEEEEEEEECCEEEEEEEEEECCCCCHHHHHHHHHHHHCCCCCCC----CCCCCCCCCC-CEEEEECCCEEEECCCCCCCCCCCCCCCC-------------------------CCCCCCCC--CCCCCCCCEEEECCC-CCCCCCCCEEEECCCCHHHCC-----CCCEEEEEEE--CHHHHHHHHCCCCCC----CCCCCCCEEEEEEEEC------ >P1;d4r3fa- ---------CCCCCCCCEEEEEEC-----CCCEEEEECCCCCHHHHHHHHHHHH---------C------CCCCCCCEEEEECCCEEEECCC-CCCCCCCCCCCHHHCCCCCCCCCCHHHCCHHHCCCCCCCCCCCCCC-CCCCCCCCEEEECCCCCCCCCCCCEEEECCCCHHHCC-----CCCEEEEECCCCCHHHHHHHCCCCCC---CCCCCCCCCCCEEEEEEEECCCCC PSA >P1;d1v9ta- -------------42723030405-----1660202005950550061015007-----------7----5104800004035a3000000025-9065337----------------------------841500051-b170-4411000109b8442020200000470871237b9730300004038--1291036007282564a737400493000540522b----- >P1;d1w74a- -------------63331010303-----3650501001810570070021005074b0856007858864003602004037830010000-623283--3042--------------------------71712328-715055310000119-695201010000057067138-----71000030558903810370062915----ca44077603064060a------ >P1;d1x7fa1 -----------------------------426040602a-------704---------------9103400371403030853741020080166069580542a-----------------------------------05-40530000000451c74-2000000056------18526500100500-98227----2077084-----------73502047-------- >P1;d1zx8a1 -----------------3020406-----43601050668--250053058---------------------50616160424760030704061674265----8408-------------------------------------6220003156------400000125043-a7405057300103046----5430708---------------67080303509-----d >P1;d2b71a1 699417513740675204020204-----2750203020630120000003007---------5------3104801004035930000003-62518407011b-------------------------840612329-515075300000018-786201010000036077025-----7100003027--52700650181916----b944056502055035------- >P1;d2mvza- --------------67320202053----8060403034c205500620250056---------------520671404506346100010259-----------------------------929030935030015857170-6500000006-776502000000054367216-----5000004046--228204807---------------b3050540403547--- >P1;d2phcb1 ------------------------------47020001ba104007400951--------a273950291013-6060460557010302504760---20552b-----------------------------------63970440000007--------740000055------1630--11000201-460027b7a5404054-----------a37040433---b707 >P1;d2wfia- -------------a3-24010200178961840102003530550040010002054a507----7275702056-20040355510101010554281000031-------------------------73080235--736055410000018-993200010000045067235-----7200003046--04800350061814b----8230614020350233------ >P1;d4r3fa- ---------ea0080401020204-----4540302000710400020004004---------5------4304602003034820010002-616293070101505419ab42033a708ca035890610401339-503064500000016a684202010000046047038-----610000200b9823830250082924---bc553058104056041374117f Translating the sequences -------------****EEEEEEC-----C*EEEEEECCCCCHHHHHHHHHHH*-----------*----CCCCC**EEEEECCCEEEECCC*C-CCCCCCC----------------------------*CCCCC***-CCCC-CCCEEEECCC*CCCCCCCCEEEECCCC***CC*****CC*EEEEE**--CHHHH**H*CCC************CCC*EEEEEE**----- -------------****EEEEEEC-----C*EEEEEECCCCCHHHHHHHHHHH*****************CCCCC**EEEEECCCEEEECCC-C*CCCC--CCC*--------------------------CCCCC***-CCCC*CCCEEEECCC-CCCCCCCCEEEECCCC***CC-----CC*EEEEE*****HHHH**H*CCCCC----******CCCEEEEEEE*------ -----------------------------C*EEEEEECC-------***---------------********CCC*******CCCEEEECC*****CCCCCCCC*-----------------------------------CC-C*CCCEEEE*C******-CCCEEEECCC------*****C**EEEEE*-***HH----H***CCC-----------CCEEEEE*-------- -----------------*EEEE*C-----C*EEEE**CCC--*HHHHHHHH---------------------*CC**EE*EECCCEEEE*CC*C*CCCC**----****-------------------------------------CC*EEE****------C*EEEECCCC**-CC*****CC*EEEE***----*******---------------CCCEEEEEE**-----* *****************EEEEEEC-----C*EEEEEECCCCCHHHHHHHHHHH*---------*------CCCCC**EEEEECCCEEEECCC-C*CCCCCCCCC*-------------------------*CCCCC***-CCCC*CCCEEEECCC-CCCCCCCCEEEECCCC***CC-----CC*EEEEE**--CHHHH**H*CCCCC----******CCCEEEEEE*------- --------------***EEEEEEC*----C*EEEEEECCCCCHHHHHHHHHHH**---------------CCCCC*******CCCEEE*CCC*C-----------------------------********CCCCC****CCCC-CCCEEEECCC-CCCCCCCCEEEECCCC***CC-----CC*EEEEE**--CHHHH****---------------CCC*EEEEEE****--- ------------------------------*EEEEEECCCCC**HHHHHHHH--------***********CC-C**EEEEECCCEEEE*CC****---CCCCC*-----------------------------------C****CCCEEEE*C--------C*EEEECCC------****--C*EEEE**-**C********CCCCC-----------CCEEEEEEE---**** -------------**-*EEEEEE********EEEEEECCCCCHHHHHHHHHHH********----*****CCCCC-*EEEEECCCEEEECCC*C*CCCCCCCCC*-------------------------*CCCCC**--CCCC*CCCEEEECCC-CCCCCCCCEEEECCCC***CC-----CC*EEEEE**--CHHHH**H*CCCCC*----*****CC*EEEEEEE*------ ---------********EEEEEEC-----C**EEEEECCCCCHHHHHHHHHHH*---------*------CCCCC**EEEEECCCEEEECCC-C*CCCCCCCCC***************************CCCCC***-CCCC*CCCEEEECCC*CCCCCCCCEEEECCCC***CC-----CC*EEEEE****CHHHH**H*CCCCC---*******CCC*EEEEEE******* 50891.tem _________________________________ -------------****EEEEEEC-----C*EEEEEECCCCCHHHHHHHHHHH*---------*-*****CCCCC**EEEEECCCEEEECCC*C*CCCCCCCCC*-------------------------*CCCCC***-CCCC*CCCEEEECCC*CCCCCCCCEEEECCCC***CC****-CC*EEEEE****CHHHH**H*CCCCC----******CCCEEEEEEE*------ Structural block scores 0 12 - 4.6 H 75.0 75.0 75.0 75.0 4.8 75.0 75.0 75.0 53.8 13 16 * 3.0 P 3.8 3.8 75.0 75.0 3.5 22.8 75.0 22.6 3.0 17 22 E 4.4 M 1.7 0.8 75.0 1.5 1.3 1.0 75.0 1.2 0.8 24 28 - 4.6 H 75.0 75.0 75.0 75.0 75.0 60.6 75.0 6.2 75.0 31 36 E 4.8 H 1.7 1.8 2.7 2.0 1.7 2.2 1.5 1.2 1.5 37 41 C 4.7 H 3.8 2.0 47.5 34.0 2.2 4.3 4.8 2.2 1.6 42 52 H 4.6 H 2.1 2.0 55.5 16.2 0.5 2.3 9.5 1.4 0.9 54 62 - 4.3 M 75.0 4.6 75.0 75.0 75.0 67.3 52.2 20.2 75.0 65 69 * 3.5 M 61.4 7.0 1.6 75.0 75.0 75.0 3.4 5.6 75.0 70 74 C 4.6 H 3.6 2.6 3.0 32.2 3.2 4.0 17.0 2.6 3.4 75 76 * 1.3 P 0.0 1.0 1.5 3.5 0.5 2.5 3.0 38.5 1.0 77 81 E 4.3 M 1.4 1.4 3.2 2.6 1.4 3.0 3.0 1.4 1.2 82 84 C 5.0 H 6.2 6.0 4.7 5.7 5.7 4.3 4.0 5.0 4.7 85 88 E 4.9 H 0.0 0.2 0.8 0.8 0.0 0.2 1.0 0.5 0.2 89 91 C 4.7 H 0.0 0.0 2.7 3.7 1.0 1.0 2.3 0.7 0.7 95 103 C 4.4 M 20.3 19.2 4.3 28.3 3.0 75.0 26.6 2.0 3.1 105 129 - 4.6 H 75.0 75.0 75.0 63.8 75.0 55.3 75.0 75.0 5.3 131 135 C 4.4 M 2.0 3.6 75.0 75.0 2.6 1.6 75.0 2.6 1.2 136 138 * 2.9 P 2.0 4.3 75.0 75.0 4.7 4.7 75.0 27.7 5.0 140 143 C 4.5 M 4.9 3.2 21.0 75.0 2.8 3.8 6.2 4.0 2.0 145 147 C 4.9 H 3.0 3.0 2.7 27.7 2.7 3.7 2.7 3.3 3.0 148 151 E 4.9 H 0.2 0.0 0.0 0.5 0.0 0.0 0.0 0.0 0.0 152 154 C 4.3 M 3.3 3.7 1.3 3.0 3.0 2.0 27.3 3.0 2.3 156 163 C 4.4 M 2.8 3.0 12.7 56.8 3.1 3.4 57.6 3.0 2.9 164 167 E 5.0 H 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 168 171 C 4.9 H 2.8 3.0 21.5 2.0 2.2 3.0 21.2 2.2 2.5 172 174 * 2.4 P 5.3 4.7 75.0 27.3 4.7 5.0 75.0 5.0 3.7 175 176 C 4.5 M 2.5 5.5 75.0 8.8 3.5 3.5 75.0 4.0 5.5 177 180 * 3.6 M 8.6 75.0 4.0 2.2 75.0 75.0 2.5 75.0 75.0 182 183 C 4.7 H 1.5 4.0 2.5 5.0 4.0 2.5 38.0 4.5 3.5 185 189 E 4.9 H 0.8 0.6 1.2 0.8 0.6 0.8 0.4 0.6 0.4 190 193 * 2.6 P 40.2 6.8 23.0 40.0 39.8 40.0 21.5 40.0 7.1 195 198 H 4.3 M 3.0 3.0 39.8 21.8 2.2 3.0 5.1 3.0 3.5 199 200 * 1.6 P 4.5 5.0 75.0 3.5 5.5 6.0 8.8 4.0 3.5 203 207 C 4.3 M 4.8 4.6 5.2 75.0 5.0 75.0 2.6 4.0 5.0 208 211 - 4.6 H 6.9 75.0 75.0 75.0 75.0 75.0 75.0 59.1 59.1 212 217 * 3.3 M 3.0 6.3 75.0 75.0 5.6 75.0 75.0 15.7 5.1 218 220 C 4.7 H 4.0 4.3 28.3 4.3 3.7 4.8 29.5 1.7 3.0 221 227 E 4.7 H 2.3 2.7 13.3 2.7 2.9 2.6 3.0 2.1 2.9 229 234 - 4.2 M 64.4 75.0 75.0 64.8 75.0 40.2 29.2 75.0 7.1 >>>>>>