Reading input alignment file to find conserved blocks of secondary structure The input structure based alignment from Comparer _____________________________________________ >P1;d1jh6a- ---------------------------CCCCCCEEEEEEEEECC----CCHHHHHHHHHHHHH-----------------------H--HCCCCCC---CCEEEEEEE--EEC----------HHHHHHHHHHHHH---CCCCEEEEEEEEEEEEEC--CEEEEEEEC-CCHHHHHHHHHHHHHC---CCCC-C-C----CCCCEEEEEC-CCCC-------HHHHHHHHHHHHHHCCCCCCCEEEEEEEEEEECCCCCCCCCCCEEEEEEECCC------- >P1;d1vgja- ----------------------------------CEEEEEECCH----HHHHHHHHHHHHHCC----------------------CC--EEEEECCHHHCEEEEEEEE--CCC----------HHHHHHHHHHHHHHHCCCCCEEEEEEEEEEEECCCCEEEEEEEEE-CCHHHHC-CHHHHHHHHCCCCCC-C-C----CCCCEEEEEE-EEEE---------CCHHHHCCCHHH-CCCEEEEEEECEEEEEEEE-EECCEEEEEEEEEEECCC------- >P1;d2fsqa1 CCCCHHHHCHHHCCCCCCCCCCCCCCCCCCCCCCEEEEECCCCC--CCHHHHHHHHHHHHHHC---------------------CHHHH--EEECCHHHCCCCEEEEECCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHCCCCCCCCCCCCCCC-----CCCCCCC---HHHHHHHHHHHHHHHHHHCCCCCCHH----HCCCCCCCEEECCCCCHHHHHHHHCCHHHHHHHHHHCC------CCCCCCEEEEEC-----CCCCEEEEECC---------- >P1;d5ae0a- ------------------------------CCCCCCEEEEEECHHHHHHHHHHHHHHHHHHHHCHHHHHHHHHCCCCCCCCCCCCHHHHCC-CCCC-CCCEEEEEE-----CHHHCCC-----CHHHHHHCHHHHHHCC--CEEEEEEEEEEECC-----CEEEEEEECC--------HHHHCCCCCCCCCCHHHCCCCCCCCCEEEEEECC---CCCCCHHHHHHHHHHHHHCCCCCC--CCCEEECCEEEEEEE---CCEEEEEEEEEEEEEEEEEEECC >P1;d5h7fa- -----------------------------CCCCEEEEEEEECCH----HHHHHHHHHHCCCC----------------------------CCEECCHHHCEEEEEEEE--EEC----------HHHHHHHHHHHHHHHCCCCCEEEEEEEEEEECC-CCCCEEEEEEE--CCCHHHHHHHHHHHHHHCCCCC-CCC----CCCCEEEEEE-CCCC---------C------CC----CCCCCCEEEECEEEEEEEE-----CCEEEEEEEEECCCCCC---- >P1;d5ldqa- -----------------------------C-CCEEEEEEEECCH----HHHHHHHHHHHHHCC---------------------HHH--C--EECCHHHCEEEEEEEE--EEC----------HHHHHHHHHHHCCC--CCCCEEEECCEEEEEC---CCCEEEEECCCCCHHHHHHHHHHHHHHHHCCCCC-CCC----CCCCCEEEEECCCCC---------C-----CCC----CCCCCCEEEECEEEEEEEE-EECCEEEEEEEEEEECCC------- PSA >P1;d1jh6a- ---------------------------7a587422000001018----a12440470064026-----------------------5--1912815---000300409--701----------7550651055008---816004030450011960--130000205-6485036006503730---809a-6-9----9150200000-0607-------99517601730372188058250302200002064925708517445428078------- >P1;d1vgja- ----------------------------------5000003057----800530381086056----------------------81--0506217372010400402--807----------a93165028205600462712603031081536698051010606-5275035-052016402719195-7-9----c170201005-0662---------465a60310871-5955062050400001425-729a5573543241504a------- >P1;d2fsqa1 16a6067004851a760842862036918036030000020048--a2a01710450165035---------------------71193--000133700110040014442544200881659170950083059407904a16a284124010-----3026117---98038106500410082070416608----90533220020061074910651180771277059506------516440000318-----24716202317---------- >P1;d5ae0a- ------------------------------dc710110001037a1045019201500430061a1058205600dad36c841504a207-441a-c30102005-----0232938-----90780062a1086048--54070002000002-----6000010406--------a5038010d49972e317c07801200000001a---a094720030003011405f73bf--714660770600118---901000509b525060304055c >P1;d5h7fa- -----------------------------a89326000006029----a0171038009508----------------------------607415481010300303--503----------38215303600671059223060306305354c-c7361020506--0a2077005601610983a0b2-718----8080301005-0780---------8------05----9291a42050620001314-----8461552260605377a---- >P1;d5ldqa- -----------------------------b-9445000003047----802540270187306---------------------890--1--6515281010300503--606----------4a317600740360--7060150405202035---9650010026922810330064025104729191-2c7----706130000360397---------2-----a12----8059703150540000117-648974615424427067------- Translating the sequences ---------------------------**CCCC*EEEEEEE*C*----**HHHHHHHHHHH**-----------------------H--*****CC---C*EEEEEEE--**C----------HHHHHHHHHHHHH---CCCCEEEEEEEEEEE***--**EEEEEE*-CCHHHHHHHHHHHHH*---CCCC-C-C----CCCCEEEEE*-CCCC-------****HHHH*******CCC*CCEEEE*EEEEEE*****CC****EEEEEEECCC------- ----------------------------------*EEEEEECCH----HHHHHHHHHHHHH**----------------------**--***EECCHHHCEEEEEEEE--**C----------HHHHHHHHHHHHHH**CCCCEEEEEEEEEEE*******EEEEEE*-CCHHHH*-*HHHHHHHH*CCCCC-C-C----CCCCEEEEEE-****---------C*HHHH******-CCC***EEEECEEEEEEEE-**CC**EEEEEEEEECCC------- *****************************CCCC*EEEEE**CC*--**HHHHHHHHHHHHH**---------------------**H**--*EECCHHHC***EEEEE****C*************HHHHHHHHHHH***CCC***********C-----C******---*HHHHHHHHHHHHHHH**CCCC*C**----*CCC****EE*CCCC*********C*HHHH*******C------***C**EEEEE*-----****EEEEE**---------- ------------------------------CCC***EEEEE*CH****HHHHHHHHHHHHH*************************H****-**CC-**CEEEEEE-----*******-----*HHHHHH*HHHHHH**--C*EEEEEEEEEE*C-----CEEEEEE**C--------HHHH*****CCCCC***C****CCCCEEEEEE*C---***********HHHH*******CC--CC*EEEC*EEEEEEE---CC**EEEEEEEEE********** -----------------------------CCCC*EEEEEEECCH----HHHHHHHHHH****----------------------------**EECCHHHCEEEEEEEE--**C----------HHHHHHHHHHHHHH**CCCCEEEEEEEEEEEC*-***CEEEEEE*--C**HHHHHHHHHHHHH*CCCCC-C*C----CCCCEEEEEE-CCCC---------C------**----CCC*CCEEEECEEEEEEEE-----**EEEEEEEEECCC***---- -----------------------------C-CC*EEEEEEECCH----HHHHHHHHHHHHH**---------------------**H--*--EECCHHHCEEEEEEEE--**C----------HHHHHHHHHHH***--CCCCEEEE**EEEEEC---**CEEEEE***CCHHHHHHHHHHHHHHH*CCCCC-C*C----CCCC*EEEEE*CCCC---------C-----***----CCC*CCEEEECEEEEEEEE-**CC**EEEEEEEEECCC------- 55144.tem _________________________________ -----------------------------CCCC*EEEEEEECCH----HHHHHHHHHHHHH**---------------------**H--***EECCHHHCEEEEEEEE--**C----------HHHHHHHHHHHHHH**CCCCEEEEEEEEEEEC*--**CEEEEEE*-CCHHHHHHHHHHHHHHH*CCCCC-C*C----CCCCEEEEEE*CCCC-------**C*HHHH*******CCC*CCEEEECEEEEEEEE-**CC**EEEEEEEEECCC------- Structural block scores 0 28 - 4.5 M 70.4 75.0 4.7 75.0 75.0 75.0 29 32 C 4.4 M 6.0 75.0 2.2 27.0 7.6 24.9 34 40 E 4.7 H 0.4 1.1 0.3 0.4 1.7 1.1 41 42 C 4.5 M 0.5 2.5 2.0 1.5 1.0 2.0 44 47 - 4.3 M 75.0 75.0 40.6 3.9 75.0 75.0 48 60 H 4.8 H 3.3 3.2 3.1 2.3 3.4 3.6 61 62 * 1.4 P 4.0 5.5 4.0 3.0 41.5 3.0 63 83 - 4.5 M 75.0 75.0 75.0 5.3 75.0 75.0 84 85 * 3.0 P 75.0 41.5 4.0 2.5 75.0 8.5 87 88 - 4.1 M 75.0 75.0 6.0 6.2 75.0 75.0 89 91 * 2.7 P 3.7 1.7 50.0 27.3 27.0 50.3 92 93 E 4.1 M 5.0 4.0 0.0 4.0 5.5 5.5 94 95 C 5.0 H 3.0 4.0 2.0 5.8 3.0 3.0 96 98 H 4.2 M 75.0 4.0 3.3 30.2 4.3 3.7 100 107 E 4.6 H 2.0 1.4 0.9 19.8 1.2 1.5 108 109 - 4.5 M 75.0 75.0 4.0 75.0 75.0 75.0 110 111 * 1.4 P 3.5 4.0 3.0 37.5 2.5 3.0 113 122 - 4.3 M 75.0 75.0 3.8 40.0 75.0 75.0 123 136 H 4.7 H 8.7 4.1 4.3 4.1 3.2 3.7 137 138 * 2.7 P 75.0 2.0 3.5 6.0 2.5 75.0 139 142 C 4.5 M 3.8 4.0 5.9 39.8 4.0 3.2 143 153 E 4.4 M 1.6 2.6 3.6 0.8 2.8 2.0 156 157 - 4.1 M 37.5 7.5 75.0 75.0 43.8 75.0 158 159 * 3.0 P 38.0 4.0 75.0 75.0 5.0 7.5 161 166 E 4.4 M 0.3 1.3 2.8 0.2 1.3 0.5 169 170 C 4.2 M 5.0 3.5 42.0 40.5 37.5 2.0 171 185 H 4.5 M 8.1 7.7 2.9 36.8 3.6 2.5 187 191 C 4.8 H 20.5 5.0 2.4 6.2 5.4 4.4 196 199 - 4.5 M 75.0 75.0 75.0 6.9 75.0 75.0 200 203 C 4.9 H 3.8 5.1 4.2 0.8 4.0 3.5 204 209 E 4.5 M 0.3 1.3 1.5 0.0 1.5 1.0 211 214 C 4.3 M 3.2 3.5 1.8 58.9 3.8 4.8 215 221 - 4.1 M 75.0 75.0 4.6 4.6 75.0 75.0 222 223 * 3.4 M 9.0 75.0 1.0 1.5 75.0 75.0 226 229 H 4.3 M 3.5 5.4 4.2 1.0 75.0 75.0 230 236 * 2.2 P 3.3 13.6 4.7 6.1 54.3 44.8 237 239 C 4.6 H 5.3 6.3 52.0 36.3 6.7 4.3 241 242 C 4.2 M 5.0 3.0 75.0 4.0 7.2 3.5 243 246 E 4.4 M 2.0 1.8 21.8 4.0 1.8 2.2 248 255 E 4.7 H 1.2 1.5 2.0 2.9 1.4 1.6 257 258 * 3.4 M 5.5 4.5 75.0 75.0 75.0 5.0 259 260 C 4.3 M 6.0 9.8 75.0 4.5 75.0 8.5 261 262 * 1.0 P 4.0 5.0 3.0 0.5 6.0 5.5 263 271 E 4.7 H 4.4 3.8 3.2 4.2 3.7 3.9 272 274 C 4.2 M 5.0 4.8 75.0 2.0 2.7 4.3 275 281 - 4.3 M 75.0 75.0 75.0 4.2 46.4 75.0 >>>>>>