Reading input alignment file to find conserved blocks of secondary structure The input structure based alignment from Comparer _____________________________________________ >P1;d1b5ea- CCCCCCCHHHHHHHHHHHHHCCCCE--ECCCC-------CEEEEEEEEEEECC-----CCCCCCCCCHHHHHHHHHHHH-HCCCCHHHCCCCCCHHHHHHCCC-------------CCCCCCCHHHHHHC------------HHHC--------------------------CHHHHHHHHHHHCCCCCCCEEECCCCCHHHHHHHHHCCCCCCEEEEEEEEE-CCEEEEEEEEEEEECCHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCEEEEEEEEEEEEEEEHHHHHHHHHHHHHC-----CCCCCC-----CCC------------------------------- >P1;d1bkpa- ----CCHHHHHHHHHHHHHHHCEECCCCCCCEECCCCCCCCEEEEEEEEEEECC-CCCCCCCCCCCCHHHHHHHHHHHHCCCCCCHHHHHCCCCCCCHHHCCC-------------CCCCCCCCHHHHHCCCEEEC-------------------------C-------EEECHHHHHHHHHHHCCCCCCCEEECCCCCCHHH-----CCCCCCEEEEEEEEE-CCEEEEEEEEEEEECCCCHHHHHHHHHHHHHHHHHHHC-------CEEEEEEEEEEEEEEEHHHHHHHHHHHHCCCCCCCEEEECCCCC---------CHHHCCHHHEEEECCCCCCCCCCCCEE >P1;d3v8ha- -------CHHHHHHHHHHHHHCEEE--CC--C-------CCEEEEEEEEEEEEHHHCCCCCCCCCCCHHHHHHHHHHHH-CCCCCHHHHHHCCCCCCHHHHHCCHHHHCCCCCC-CCCCCCCCCHHHHHHEEEEEEEECCCHHHHHHHHHCCCEEEEEECCCCCEEEEEEEECHHHHHHHHHHHCCCCCCCEEECCCHHHHHH-----CCCCCCEEEEEEEECCCCCEEEEEEEEEEECCCCHHHHHHHHHHHHHHHHHHHC-------CCEEEEEEEEEEEEEEHHHCCCC--CCCC-CC-CCEEEECCCCCHHHHCCCCCHHHHCCHHHEEEECCCCC--------- >P1;d4ez8a- ----CCCHHHHHHHHHHHHHHCEEE--CCCCC-------CCEEEEEEEEEEEECCCCCCCCCCCCCCHHHHHHHHHHHH-CCCCCHHHHHCCCCCCCCCCCC-HHHHHHCCCCCCCCCCCCCCHHHHHHHCCCCCC----------CCCCCCC---------------CCCCCHHHHHHHHHHHCCCCCCCEEECCCCCCHHH-----CCCCCCEEEEEEEEE-CCEEEEEEEEEEEECCCHHHHHHHHHHHHHHHHHHHHC-------CEEEEEEEEEEEEEEEHHHHHHHHHHHCCCCCCCCEEEECCCCC---------CHHHCCHHHEEEECCCCCCCCCCCCCC PSA >P1;d1b5ea- 848a144065005400311677725--72878-------45001279050205-----342001634971262014004-5422509504ba02841673008-------------75100100010011------------9709--------------------------310660273029548088030503296079346549051304032030203-a65000204042010044011113003300540173038859927071140104083010126011002113646-----725157-----974------------------------------- >P1;d1bkpa- ----410073018006301670722777b1460585755021221872305060-73000000150616200200000004122306302828065048534b-------------71201401030024554729-------------------------b-------86102031013105654919604030327912b5-----012304013030307-a8402030403202004500110000000010003009-------18203000201502014302910540192823a00804026909---------5036072a1060480724a81805709 >P1;d3v8ha- -------085004004502870838--86--d-------5410218815041105810000002706192000000000-3002305603819084038304859a03828517-782100300010006222544151839a71750376516245757cc48203032433104600410265292990303030681383-----004303013020405795102030503201005500110000000020002001-------16223000404601034713b60--01a5-54-206050550222685824050055042900605b1733--------- >P1;d4ez8a- ----a24034007105500760956--82609-------2002028715060404a30000000505150001000000-7010205602855073245104-3a20474917b1640000010000012371706----------5073908---------------c5254104700620486492980403030680274-----002303114030607-a820204040320200450011000000001000200a-------28101010200200004602820560182713800404044507---------606405580060590801771807416 Translating the sequences ****CC*HHHHHHHHHHHHH*C**E--*CCCC-------C*EEEEEEEEEE**-----CCCCCCCCCHHHHHHHHHHHH-*CCCCHHH**CCCC***HHHCCC-------------CCCCCCC*HHHHH*------------****--------------------------CHHHHHHHHHHHCCCCCCCEEECCCCC*HHH*****CCCCCCEEEEEEEEE-CCEEEEEEEEEEEECC**HHHHHHHHHHHHHHHHHHH********CEEEEEEEEEEEEEEEHHHHHHHHHHH**C-----****CC-----***------------------------------- ----CC*HHHHHHHHHHHHHHCEE***CCCC********CCEEEEEEEEEEE**-*CCCCCCCCCCCHHHHHHHHHHHH*CCCCCHHHHHCCCCCCCHHHCCC-------------CCCCCCC*HHHHH*******-------------------------*-------***CHHHHHHHHHHHCCCCCCCEEECCCCC*HHH-----CCCCCCEEEEEEEEE-CCEEEEEEEEEEEECCC*HHHHHHHHHHHHHHHHHHHC-------CEEEEEEEEEEEEEEEHHHHHHHHHHH*CCCC*CCEEEECCCCC---------*HHHCCHHHEEEECCCCC********* -------*HHHHHHHHHHHHHCEEE--CC--C-------CCEEEEEEEEEEE****CCCCCCCCCCCHHHHHHHHHHHH-CCCCCHHHHH*CCCCCCHHH**C***********-*CCCCCCC*HHHHH*******************************************CHHHHHHHHHHHCCCCCCCEEECCC***HHH-----CCCCCCEEEEEEEE**CC*EEEEEEEEEEECCC*HHHHHHHHHHHHHHHHHHHC-------C*EEEEEEEEEEEEEEHHH****--***C-CC-CCEEEECCCCC**********HHHCCHHHEEEECCCCC--------- ----CC*HHHHHHHHHHHHHHCEEE--CCCCC-------CCEEEEEEEEEEE****CCCCCCCCCCCHHHHHHHHHHHH-CCCCCHHHHHCCCCCCC***CC-*************CCCCCCC*HHHHH*******----------*******---------------****CHHHHHHHHHHHCCCCCCCEEECCCCC*HHH-----CCCCCCEEEEEEEEE-CCEEEEEEEEEEEECCC*HHHHHHHHHHHHHHHHHHHC-------CEEEEEEEEEEEEEEEHHHHHHHHHHH*CCCC*CCEEEECCCCC---------*HHHCCHHHEEEECCCCC********* 55831.tem _________________________________ ----CC*HHHHHHHHHHHHHHCEEE--CCCCC-------CCEEEEEEEEEEE****CCCCCCCCCCCHHHHHHHHHHHH-CCCCCHHHHHCCCCCCCHHHCCC***********-*CCCCCCC*HHHHH*******------***********--------*------****CHHHHHHHHHHHCCCCCCCEEECCCCC*HHH-----CCCCCCEEEEEEEEE-CCEEEEEEEEEEEECCC*HHHHHHHHHHHHHHHHHHHC-------CEEEEEEEEEEEEEEEHHHHHHHHHHH*CCCC*CCEEEECCCCC--***----*HHHCCHHHEEEECCCCC********* Structural block scores 0 3 - 4.3 M 7.6 75.0 75.0 75.0 4 5 C 4.3 M 2.5 2.5 75.0 6.2 7 20 H 4.9 H 2.7 3.0 3.1 2.7 22 24 E 4.3 M 4.7 3.7 6.3 6.7 25 26 - 4.3 M 75.0 7.0 75.0 75.0 27 31 C 4.4 M 6.4 5.9 35.5 5.0 32 38 - 4.3 M 75.0 5.0 75.0 75.0 39 40 C 4.7 H 4.5 1.0 4.5 1.0 41 51 E 4.9 H 2.4 2.8 2.8 2.8 52 55 * 2.3 P 57.5 22.0 3.5 4.6 56 66 C 4.9 H 15.7 1.4 1.5 1.2 67 78 H 5.0 H 3.0 0.9 1.0 0.6 80 84 C 4.9 H 3.6 2.4 1.6 2.0 85 89 H 4.7 H 3.6 2.2 2.8 2.6 90 96 C 4.6 H 5.3 4.1 4.3 4.3 97 99 H 4.3 M 5.3 5.7 4.7 3.3 100 102 C 4.3 M 2.7 6.2 4.0 26.3 103 113 * 3.5 M 75.0 75.0 5.3 5.4 116 122 C 5.0 H 2.0 2.1 2.0 0.7 124 128 H 5.0 H 0.4 1.0 0.2 0.2 129 135 * 2.1 P 64.4 5.1 3.6 3.7 136 141 - 4.3 M 75.0 75.0 4.5 75.0 142 152 * 3.5 M 50.0 75.0 4.8 30.2 153 160 - 4.3 M 75.0 75.0 6.1 75.0 162 167 - 4.3 M 75.0 75.0 2.8 75.0 168 171 * 2.6 P 75.0 22.5 3.0 6.1 173 183 H 5.0 H 3.3 2.0 2.2 2.9 184 190 C 5.0 H 4.7 4.9 5.1 5.4 191 193 E 5.0 H 2.7 2.3 2.0 2.3 194 198 C 4.7 H 4.0 4.2 3.4 3.4 200 202 H 5.0 H 6.3 6.2 4.7 4.3 203 207 - 4.3 M 5.6 75.0 75.0 75.0 208 213 C 5.0 H 2.2 1.7 1.7 1.3 214 222 E 4.9 H 1.4 1.9 1.7 2.4 224 225 C 5.0 H 8.2 9.2 7.0 9.2 226 237 E 4.9 H 1.5 1.7 1.4 1.6 238 240 C 4.8 H 1.3 1.3 1.7 1.3 242 260 H 5.0 H 1.7 0.3 0.3 0.3 262 268 - 4.3 M 6.9 75.0 75.0 75.0 270 284 E 5.0 H 2.1 1.6 2.1 1.0 285 295 H 4.5 M 1.5 2.6 16.7 3.1 297 300 C 4.3 M 40.0 3.8 22.2 3.2 302 303 C 4.3 M 75.0 0.0 1.0 0.0 304 307 E 4.3 M 3.8 3.0 2.8 2.0 308 312 C 4.6 H 47.4 5.2 2.8 4.0 313 314 - 4.3 M 75.0 75.0 4.0 75.0 315 317 * 3.5 M 6.7 75.0 7.0 75.0 318 321 - 4.3 M 75.0 75.0 2.8 75.0 323 325 H 4.3 M 75.0 3.0 3.3 3.3 326 327 C 4.3 M 75.0 3.5 2.0 2.5 328 330 H 4.3 M 75.0 4.5 3.7 4.3 331 334 E 4.3 M 75.0 2.5 2.8 2.8 335 339 C 4.3 M 75.0 4.2 5.1 3.6 340 348 * 3.5 M 75.0 5.4 75.0 4.6 >>>>>>