Reading input alignment file to find conserved blocks of secondary structure The input structure based alignment from Comparer _____________________________________________ >P1;d1zn6a1 CCCEEE-CCCCCCCCCCC-EEC--CC--------CCCC-CCCC---CCEECCCCCCCCEECEECEEC-CCC---CCC-----------------HHHHHHHHHCCCCCCCCCCCCC-CCCCHHHHHCCCEEEEEEEEEEEEECCC----CCCEEEEEEECCCCCEEEEEEEEEEEC----C---CC-CEEEEEE-CCCCCCCCCCHHHCCCCCCCCCCCCCCHHHHHHHHH--CCHHHHHHHC--CCCCHHHEEEEECC------------------ >P1;d2aega1 CCCEEC-CC-CCHHHHCCCCEE--CCC--------CCCCCCCC---CCEEEEECCCCCEEEEECEECCCCCHHHHHHHHHHHHHHHHCCCCCCCHHHHHCCCCCCCCEECCC---C-CHHHHHHCCHHHEEEECCCEEEEECCCCCCCCCCCCEEEEECCCCCCCCEEEEEEEEEEECCCH--HHCCEEEEEEEEECCCC--CCCCCCCCC---CCCCCCCCHHHHHHCC---CCHHHHHHHC--CCCCCCCCEEEEEECCCCCCC----------- >P1;d2bdva1 CCCEEECCCHHHHHHHHCC---CCCCC------CCCEEEECCC--CCCEECCCC-CCCCCCEECCCCCCCC------------------------------CCCCCCEEEHHHHHCCCCCCCCCC--CCEEEEEEEEEEEEEECCCCCCCCEEEEEEEE-E-EEEEEEEEECC---CCCCCCCHHH-----CEEEEEC-HH--HCCCCCC---CCCCCCCCCHHHHHHHHCCCCCHHHHHHHHC-CCCCHHHCEEEECCCCCC------CCCCCCCC >P1;d2f20a1 CCEEEC-CCHHHHHHHCC-CCC--HHHHHCHHHHCCCCCEEHHHCCEEEECCCCC----CCEEEEECCCCC---CCC----------------CHHHHHHHCC--CCEEEHHHCCC-CCCCCCCCC--CEECCCCCEEEEEEEEC----CEEEEEEECCCC-CCCCCCEEEEEEEC----C--CCC-CEEEEEEEEECCC--CHHHHHHCC-CC-CCCCCCCHHHHHHHCCCCCCHHHHHHCC--CCCCCCC-CEEECCHHHHHCCCCCHHHHCCC- >P1;d2icua- -CCEEECCCHHHHHCCCCC---HHHCCCCCCCCCCCEEEECCC--CEEEEEEEE-CCEEEEEEEECCCCCC--------------------------------CCCCEEEHHHHC-CCCCHHHHH--HCEECCCCCEEEEEC----------CEEEEEECC-CCCCCCEEECC---CHHH-CCCCC-----CEEEEEEECC--HHHHHCC---C-EEECCCCHHHHHHC-CCCCCHHHHHHHHHHHCCCHHHEEEEECCHHHHCCCCCCHHHHC-CC PSA >P1;d1zn6a1 061131-03756347407-023--26--------9056-6514---62200265ba95250250100-021---b07-----------------6851970485a11304054037-6811420076120000001001032467----a84350302046a00001000114153----7---76-7441000-00241481721540259b7421000054c2087004--0529505720--75052a6061663a------------------ >P1;d2aega1 062002-27-903761088075--61c--------29340411---7400012287a8220040100001288714840674087268796a26796147020703020372---b-371057007452001000000004058438bc48411000044893500000000373621059--74733422000000171--172056028---8100002558305406---1719503710--63056a005325427693327----------- >P1;d2bdva1 0000003344850052014---b683b------6766330116--540100103-a77442530000140b------------------------------a4a842005153017555113603--800000001000004457a89a2812120031-b-71000000031---3782934543-----0000003-29--6100118---9031000033820340032817393027005-522659407354096900------7018563c >P1;d2f20a1 041002-2606610720a-162--7304734a70232100305712400001658----202004000004---408----------------45a6057325--10104174018-552056009--1000001100011235c----a9520110305a-09100000105060----7--848-6624000000080--283256003-38-5110103593075006790779504700--7215285-50430575048275735602375- >P1;d2icua- -510000422540073009---8a4160864685052200125--550200122-994010050100237d--------------------------------b45230525702-839235104--800000001000235----------501003156-a4000000014---5053-53864-----0001012604--6705803---8-10100042910340-378070a5047108722040740422303850585944667016-56 Translating the sequences CCCEEE-CC*******CC-***--CC--------CCCC-*CCC---CCEECCCCCCCCEECEECEEC-CCC---***-----------------HHHHH****CCCC*******CC-CCCCHHH****CEEEE***EEEEEE*CC----CC*EEEEEEECC*CC**EEEEEEEEE*----C---CC-*EEEEEE-**CCC**C*CHHHCCC**CCCCCCCCCHHHHHHH**--CCHHHHHHHC--CCCCHHH*EEEECC------------------ CCCEE*-CC-**HHHHCCC***--CCC--------CCC**CCC---CCEE***CCCCCEE*EECEECCCCC***********************HHHHH**CCCCCCEE***---C-C***HHHC****EEEECCCEEEEE**CC****CC**EEEEE*CC*CCCCEEEEEEEEE******--**C**EEEEEEEE*CCC--C*C***CCC---CCCCCCCCHHHHHH**---CCHHHHHHHC--CCCC****EEEE*******CC----------- CCCEEE*CCHHHHHHH*CC---**CCC------*CC***ECCC--CCCEECCCC-CCC**CEEC**CCCCC------------------------------CCCCCCEEEHHH**C*CCCC***C--*CEEEE***EEEEEE*CC****CC*EEEEEEE-*-****EEEEE**---****C*****-----*EEEEEC-**--HC***CC---CCCCCCCCCHHHHHHH*CCCCCHHHHHHH**-CCCCHHH*EEEECC****------****C*C* CC*EE*-CCHHHHHHHCC-***--**********CCCC*E*****C**EECCCCC----*CEE*EECCCCC---***----------------*HHHHH**CC--CCEEEHHH*CC-CCCC***C*--CEE**CCCEEEEEE**C----C**EEEEE**CC-CCCC**EEEEEEE*----C--*CC-*EEEEEEEEECCC--CH*HHH*CC-*C-CCCCCCCHHHHHHH*CCCCCHHHHHH*C--CCCC***-*EEECC*****CC*******C*C- -CCEEE*CCHHHHH**CCC---***CC*******CC***ECCC--C**EE****-CC*EE*EE*E*CCCCC--------------------------------CCCCEEEHHH*C-*CCC*HHH*--*CEE**CCCEEEEE*----------*EEEEEECC-CCCC**EEE**---****-***CC-----*EEEEE**C*--H*HHHCC---C-***CCCCHHHHHH*-CCCCCHHHHHHH****CCCHHH*EEEECC*****CC*******C-C* 143081.tem _________________________________ CCCEEE-CCHHHHHHHCCC***--CCC------*CCCC*ECCC--CCCEECCCCCCCCEECEECEECCCCC---***-----------------HHHHH**CCCCCCEEEHHH*CC-CCCCHHHC*-*CEEEECCCEEEEEE*CC----CC*EEEEEEECC-CCCCEEEEEEEEE*****C--*CC-*EEEEEEEEECCC*-CHCHHHCCC--CCCCCCCCCHHHHHHH*CCCCCHHHHHHHC--CCCCHHH*EEEECC*****CC---****C-C- Structural block scores 0 2 C 4.7 H 2.3 2.7 0.0 1.7 27.0 3 5 E 4.6 H 1.7 0.7 0.0 0.7 0.0 7 8 C 5.0 H 1.5 4.5 3.5 4.0 3.0 9 15 H 4.0 M 5.1 14.4 3.4 3.1 3.0 16 18 C 4.6 H 27.3 5.3 1.7 28.5 3.0 19 21 * 3.0 P 1.7 4.0 75.0 3.0 75.0 22 23 - 3.8 M 75.0 75.0 8.8 75.0 9.2 24 26 C 4.1 M 27.7 6.5 7.5 3.3 3.7 27 32 - 3.8 M 75.0 75.0 75.0 5.9 5.3 34 37 C 4.3 M 5.0 22.2 5.5 2.0 2.2 40 42 C 4.5 M 3.3 2.0 2.7 2.7 2.7 43 44 - 4.5 M 75.0 75.0 75.0 4.0 75.0 45 47 C 3.9 M 27.7 28.7 3.0 2.0 3.3 48 49 E 5.0 H 1.0 0.0 0.5 0.0 1.0 50 57 C 4.1 M 6.1 4.8 12.9 30.6 12.8 58 59 E 3.9 M 3.5 2.0 4.0 38.5 0.5 61 62 E 5.0 H 3.5 2.0 4.0 1.0 2.5 64 65 E 4.2 M 0.5 0.5 0.0 2.0 0.5 66 70 C 4.9 H 15.6 0.6 3.3 0.8 5.1 71 73 - 4.5 M 75.0 7.7 75.0 75.0 75.0 74 76 * 3.0 P 6.2 4.3 75.0 4.0 75.0 77 93 - 4.5 M 75.0 5.4 75.0 70.8 75.0 94 98 H 4.2 M 5.8 5.4 75.0 5.3 75.0 99 100 * 3.0 P 3.5 3.5 75.0 5.0 75.0 101 106 C 4.5 M 4.9 2.0 6.5 26.3 28.8 107 109 E 4.3 M 2.3 1.7 1.7 1.7 2.7 110 112 H 3.9 M 3.0 28.0 3.0 4.0 4.7 114 115 C 4.3 M 5.0 43.2 4.0 4.5 38.5 117 120 C 4.5 M 4.0 2.8 3.0 3.0 4.2 121 123 H 3.8 M 2.0 4.0 3.0 3.7 2.0 129 132 E 4.4 M 0.0 0.2 0.0 0.0 0.0 133 135 C 3.8 M 0.3 0.0 0.3 0.7 0.3 136 141 E 4.8 H 1.0 0.7 0.7 0.7 1.7 143 144 C 4.3 M 6.5 6.0 6.0 8.8 75.0 145 148 - 3.8 M 75.0 8.8 9.5 75.0 75.0 149 150 C 4.3 M 9.2 6.0 5.0 9.8 75.0 152 158 E 4.6 H 1.9 0.9 1.3 1.0 1.4 159 160 C 4.5 M 5.0 6.0 43.2 7.8 5.5 162 165 C 4.2 M 0.0 2.0 2.0 2.5 3.6 166 174 E 4.3 M 1.4 1.4 17.1 1.3 17.2 175 179 * 3.0 P 60.6 2.8 19.0 60.0 17.6 181 182 - 3.8 M 75.0 75.0 3.5 75.0 4.0 184 185 C 4.2 M 6.5 5.5 3.5 6.0 5.0 188 196 E 4.4 M 9.3 0.9 25.0 1.3 25.2 197 199 C 4.4 M 2.3 3.0 26.7 2.7 2.7 205 207 H 3.8 M 3.3 3.7 0.3 4.3 4.3 208 210 C 4.6 H 2.3 3.3 28.0 1.0 26.0 211 212 - 4.2 M 10.2 75.0 75.0 39.0 75.0 213 221 C 4.7 H 2.1 10.1 1.8 10.4 9.9 222 228 H 4.8 H 4.8 3.6 2.9 4.1 2.7 230 234 C 4.5 M 31.8 46.6 4.2 5.8 5.0 235 241 H 4.9 H 4.3 3.7 3.4 4.6 3.9 243 244 - 4.2 M 75.0 75.0 40.0 75.0 7.5 245 248 C 4.9 H 4.2 3.5 3.8 3.8 2.0 249 251 H 3.8 M 6.2 5.5 6.0 5.0 3.7 253 256 E 4.9 H 4.8 3.8 4.8 3.0 2.8 257 258 C 4.5 M 6.8 3.0 4.5 2.5 1.5 259 263 * 2.3 P 75.0 5.6 18.0 4.8 5.2 264 265 C 4.2 M 75.0 4.5 75.0 4.5 7.0 266 268 - 3.8 M 75.0 75.0 75.0 5.0 4.7 269 272 * 3.0 P 75.0 75.0 4.0 3.2 3.5 >>>>>>